EWAS
As
DMP_As = run_EWAS(DNAm = ComBat.Mvalues.Metals, pheno = pDatAge7Metal, var = 'As_log2', covar = c('female_d', 'race_child2', 'age_yrs_7y_blood', 'age_mom_enroll_d', 'bmi_mom_prepreg_d', 'coll_grad', 'nullip', 'gt70k', 'smk_preg', 'Bcell_S_7y', 'CD4T_S_7y', 'CD8T_S_7y', 'Neu_S_7y', 'Mono_S_7y', 'NK_S_7y'), anno = anno, path = '/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/As')
# Unadjusted, N = 333
# Unadjusted, p<0.05: 23361
# Unadjusted, FDR<0.05: 0
# Unadjusted, pBonf<0.05: 0
# Adjusted, N = 333
# Adjusted, p<0.05: 15951
# Adjusted, FDR<0.05: 0
# Adjusted, pBonf<0.05: 0
# Adjusted, lambda: 0.9103149
# Number of DMRs identified: 5
# rm(DMP_As); gc()
DMRs
|
chr
|
start
|
end
|
p
|
length
|
fdr
|
sidak
|
nprobe
|
|
2
|
113992761
|
113993313
|
0.00e+00
|
552
|
0.00e+00
|
0.0000000
|
8
|
|
3
|
46759437
|
46759698
|
0.00e+00
|
261
|
0.00e+00
|
0.0000006
|
7
|
|
17
|
1395863
|
1396123
|
0.00e+00
|
260
|
0.00e+00
|
0.0000023
|
5
|
|
1
|
228395755
|
228396009
|
0.00e+00
|
254
|
0.00e+00
|
0.0000061
|
4
|
|
17
|
75315562
|
75315667
|
2.65e-05
|
105
|
2.65e-05
|
0.0947026
|
3
|
No adjustment for fish consumption
knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/As/As_log2_QQ_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/As/As_log2_volcano_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/As/As_log2_manhattan_DMP_adj.png")

As, female
pDatAge7Metal_F = pDatAge7Metal[pDatAge7Metal$female_d == 1,]
pDatAge7Metal_F$race_child2 = as.factor(as.numeric(pDatAge7Metal_F$race_child2))
DMP_As_F = run_EWAS(DNAm = ComBat.Mvalues.Metals, pheno = pDatAge7Metal_F, var = 'As_log2', covar = c('race_child2', 'age_yrs_7y_blood', 'age_mom_enroll_d', 'bmi_mom_prepreg_d', 'coll_grad', 'nullip', 'gt70k', 'smk_preg', 'Bcell_S_7y', 'CD4T_S_7y', 'CD8T_S_7y', 'Neu_S_7y', 'Mono_S_7y', 'NK_S_7y'), anno = anno, path = '/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/As_F')
# # Unadjusted, N = 158
# Unadjusted, p<0.05: 26064
# Unadjusted, FDR<0.05: 0
# Unadjusted, pBonf<0.05: 0
# Adjusted, N = 158
# Adjusted, p<0.05: 15824
# Adjusted, FDR<0.05: 0
# Adjusted, pBonf<0.05: 0
# Adjusted, lambda: 0.9007317
# Number of DMRs identified: 4
# rm(DMP_As_F); gc()
DMRs
|
chr
|
start
|
end
|
p
|
length
|
fdr
|
sidak
|
nprobe
|
|
1
|
11561496
|
11561711
|
0.0e+00
|
215
|
0.0e+00
|
0.0000021
|
3
|
|
7
|
76027000
|
76027101
|
0.0e+00
|
101
|
0.0e+00
|
0.0000095
|
3
|
|
2
|
113992842
|
113993142
|
0.0e+00
|
300
|
0.0e+00
|
0.0000303
|
5
|
|
2
|
198651075
|
198651347
|
6.4e-06
|
272
|
6.4e-06
|
0.0092121
|
3
|
No adjustment for fish consumption
knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/As_F/As_log2_QQ_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/As_F/As_log2_volcano_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/As_F/As_log2_manhattan_DMP_adj.png")

As, male
pDatAge7Metal_M = pDatAge7Metal[pDatAge7Metal$female_d == 0,]
pDatAge7Metal_M$race_child2 = as.factor(as.numeric(pDatAge7Metal_M$race_child2))
DMP_As_M = run_EWAS(DNAm = ComBat.Mvalues.Metals, pheno = pDatAge7Metal_M, var = 'As_log2', covar = c('race_child2', 'age_yrs_7y_blood', 'age_mom_enroll_d', 'bmi_mom_prepreg_d', 'coll_grad', 'nullip', 'gt70k', 'smk_preg', 'Bcell_S_7y', 'CD4T_S_7y', 'CD8T_S_7y', 'Neu_S_7y', 'Mono_S_7y', 'NK_S_7y'), anno = anno, path = '/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/As_M')
# Unadjusted, N = 175
# Unadjusted, p<0.05: 11497
# Unadjusted, FDR<0.05: 0
# Unadjusted, pBonf<0.05: 0
# Adjusted, N = 175
# Adjusted, p<0.05: 14046
# Adjusted, FDR<0.05: 0
# Adjusted, pBonf<0.05: 0
# Adjusted, lambda: 0.8408844
# Number of DMRs identified: 6
# rm(DMP_As_M); gc()
DMRs
|
chr
|
start
|
end
|
p
|
length
|
fdr
|
sidak
|
nprobe
|
|
17
|
47091977
|
47092178
|
0.0000000
|
201
|
0.0000000
|
0.0000001
|
4
|
|
2
|
164204627
|
164205032
|
0.0000000
|
405
|
0.0000000
|
0.0000038
|
5
|
|
17
|
1395863
|
1396123
|
0.0000000
|
260
|
0.0000001
|
0.0000717
|
5
|
|
16
|
88706240
|
88706389
|
0.0000016
|
149
|
0.0000024
|
0.0042168
|
2
|
|
8
|
22735275
|
22735388
|
0.0000089
|
113
|
0.0000107
|
0.0305879
|
3
|
|
7
|
27183400
|
27183436
|
0.0062439
|
36
|
0.0062439
|
1.0000000
|
2
|
No adjustment for fish consumption
knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/As_M/As_log2_QQ_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/As_M/As_log2_volcano_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/As_M/As_log2_manhattan_DMP_adj.png")

Ba
DMP_Ba = run_EWAS(DNAm = ComBat.Mvalues.Metals, pheno = pDatAge7Metal, var = 'Ba_log2', covar = c('female_d', 'race_child2', 'age_yrs_7y_blood', 'age_mom_enroll_d', 'bmi_mom_prepreg_d', 'coll_grad', 'nullip', 'gt70k', 'smk_preg', 'Bcell_S_7y', 'CD4T_S_7y', 'CD8T_S_7y', 'Neu_S_7y', 'Mono_S_7y', 'NK_S_7y'), anno = anno, path = '/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Ba')
# Unadjusted, N = 333
# Unadjusted, p<0.05: 11801
# Unadjusted, FDR<0.05: 0
# Unadjusted, pBonf<0.05: 0
# Adjusted, N = 333
# Adjusted, p<0.05: 11716
# Adjusted, FDR<0.05: 0
# Adjusted, pBonf<0.05: 0
# Adjusted, lambda: 0.7753982
# Number of DMRs identified: 3
# rm(DMP_Ba); gc()
DMRs
|
chr
|
start
|
end
|
p
|
length
|
fdr
|
sidak
|
nprobe
|
|
17
|
6899084
|
6899577
|
0.0000000
|
493
|
0.0000000
|
0.00e+00
|
10
|
|
16
|
1583809
|
1584118
|
0.0000000
|
309
|
0.0000000
|
2.64e-05
|
6
|
|
6
|
32145616
|
32145626
|
0.0436714
|
10
|
0.0436714
|
1.00e+00
|
2
|
knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Ba/Ba_log2_QQ_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Ba/Ba_log2_volcano_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Ba/Ba_log2_manhattan_DMP_adj.png")

Ba, female
DMP_Ba_F = run_EWAS(DNAm = ComBat.Mvalues.Metals, pheno = pDatAge7Metal_F, var = 'Ba_log2', covar = c('race_child2', 'age_yrs_7y_blood', 'age_mom_enroll_d', 'bmi_mom_prepreg_d', 'coll_grad', 'nullip', 'gt70k', 'smk_preg', 'Bcell_S_7y', 'CD4T_S_7y', 'CD8T_S_7y', 'Neu_S_7y', 'Mono_S_7y', 'NK_S_7y'), anno = anno, path = '/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Ba_F')
# Unadjusted, N = 158
# Unadjusted, p<0.05: 29651
# Unadjusted, FDR<0.05: 0
# Unadjusted, pBonf<0.05: 0
# Adjusted, N = 158
# Adjusted, p<0.05: 24029
# Adjusted, FDR<0.05: 0
# Adjusted, pBonf<0.05: 0
# Adjusted, lambda: 1.224716
# Number of DMRs identified: 5
# rm(DMP_Ba_F); gc()
DMRs
|
chr
|
start
|
end
|
p
|
length
|
fdr
|
sidak
|
nprobe
|
|
17
|
6899084
|
6899577
|
0.0000000
|
493
|
0.0000000
|
0.0000000
|
10
|
|
2
|
183943387
|
183943551
|
0.0000000
|
164
|
0.0000000
|
0.0000270
|
5
|
|
17
|
37123637
|
37123949
|
0.0000000
|
312
|
0.0000000
|
0.0000168
|
9
|
|
7
|
94285269
|
94285352
|
0.0000006
|
83
|
0.0000008
|
0.0029480
|
7
|
|
11
|
111250128
|
111250201
|
0.0009145
|
73
|
0.0009145
|
0.9928711
|
3
|
knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Ba_F/Ba_log2_QQ_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Ba_F/Ba_log2_volcano_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Ba_F/Ba_log2_manhattan_DMP_adj.png")

Ba, male
DMP_Ba_M = run_EWAS(DNAm = ComBat.Mvalues.Metals, pheno = pDatAge7Metal_M, var = 'Ba_log2', covar = c('race_child2', 'age_yrs_7y_blood', 'age_mom_enroll_d', 'bmi_mom_prepreg_d', 'coll_grad', 'nullip', 'gt70k', 'smk_preg', 'Bcell_S_7y', 'CD4T_S_7y', 'CD8T_S_7y', 'Neu_S_7y', 'Mono_S_7y', 'NK_S_7y'), anno = anno, path = '/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Ba_M')
# Unadjusted, N = 175
# Unadjusted, p<0.05: 25363
# Unadjusted, FDR<0.05: 0
# Unadjusted, pBonf<0.05: 0
# Adjusted, N = 175
# Adjusted, p<0.05: 26609
# Adjusted, FDR<0.05: 0
# Adjusted, pBonf<0.05: 0
# Adjusted, lambda: 1.225518
# Number of DMRs identified: 3
rm(DMP_Ba_M); gc()
DMRs
|
chr
|
start
|
end
|
p
|
length
|
fdr
|
sidak
|
nprobe
|
|
16
|
1583809
|
1584118
|
0e+00
|
309
|
0e+00
|
0.0000000
|
6
|
|
19
|
50194119
|
50194252
|
0e+00
|
133
|
0e+00
|
0.0000052
|
5
|
|
6
|
29595001
|
29595335
|
1e-07
|
334
|
1e-07
|
0.0001322
|
8
|
knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Ba_M/Ba_log2_QQ_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Ba_M/Ba_log2_volcano_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Ba_M/Ba_log2_manhattan_DMP_adj.png")

Cd
DMP_Cd = run_EWAS(DNAm = ComBat.Mvalues.Metals, pheno = pDatAge7Metal, var = 'Cd_log2', covar = c('female_d', 'race_child2', 'age_yrs_7y_blood', 'age_mom_enroll_d', 'bmi_mom_prepreg_d', 'coll_grad', 'nullip', 'gt70k', 'smk_preg', 'Bcell_S_7y', 'CD4T_S_7y', 'CD8T_S_7y', 'Neu_S_7y', 'Mono_S_7y', 'NK_S_7y'), anno = anno, path = '/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Cd')
# Unadjusted, N = 333
# Unadjusted, p<0.05: 9428
# Unadjusted, FDR<0.05: 0
# Unadjusted, pBonf<0.05: 0
# Adjusted, N = 333
# Adjusted, p<0.05: 11856
# Adjusted, FDR<0.05: 1
# Adjusted, pBonf<0.05: 1
# Adjusted, lambda: 0.8163213
# Number of DMRs identified: 4
# rm(DMP_Cd); gc()
FDR-significant DMPs
|
|
cpg
|
logFC
|
CI.L
|
CI.R
|
AveExpr
|
t
|
P.Value
|
adj.P.Val
|
B
|
adj.P.Val.bonf
|
std_err
|
chr
|
pos
|
gene
|
end
|
|
112561
|
cg07044523
|
0.2554657
|
0.1719724
|
0.3389591
|
5.275559
|
6.019999
|
0
|
0.0019081
|
10.31706
|
0.0019081
|
0.042597
|
chr1
|
153514376
|
S100A5
|
153514376
|
DMRs
|
chr
|
start
|
end
|
p
|
length
|
fdr
|
sidak
|
nprobe
|
|
7
|
158045979
|
158046166
|
0.0000000
|
187
|
0.0000000
|
0.0000093
|
3
|
|
5
|
23507449
|
23507656
|
0.0000000
|
207
|
0.0000000
|
0.0000228
|
5
|
|
17
|
46685291
|
46685448
|
0.0000000
|
157
|
0.0000001
|
0.0001083
|
5
|
|
7
|
27184158
|
27184188
|
0.0027811
|
30
|
0.0027811
|
1.0000000
|
4
|
knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Cd/Cd_log2_QQ_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Cd/Cd_log2_volcano_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Cd/Cd_log2_manhattan_DMP_adj.png")

Cd, female
DMP_Cd_F = run_EWAS(DNAm = ComBat.Mvalues.Metals, pheno = pDatAge7Metal_F, var = 'Cd_log2', covar = c('race_child2', 'age_yrs_7y_blood', 'age_mom_enroll_d', 'bmi_mom_prepreg_d', 'coll_grad', 'nullip', 'gt70k', 'smk_preg', 'Bcell_S_7y', 'CD4T_S_7y', 'CD8T_S_7y', 'Neu_S_7y', 'Mono_S_7y', 'NK_S_7y'), anno = anno, path = '/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Cd_F')
# Unadjusted, N = 158
# Unadjusted, p<0.05: 13276
# Unadjusted, FDR<0.05: 0
# Unadjusted, pBonf<0.05: 0
# Adjusted, N = 158
# Adjusted, p<0.05: 13473
# Adjusted, FDR<0.05: 0
# Adjusted, pBonf<0.05: 0
# Adjusted, lambda: 0.8343739
# Number of DMRs identified: 7
# rm(DMP_Cd_F); gc()
DMRs
|
chr
|
start
|
end
|
p
|
length
|
fdr
|
sidak
|
nprobe
|
|
6
|
32164926
|
32165321
|
0.0000000
|
395
|
0.0000000
|
0.0000000
|
7
|
|
17
|
46685291
|
46685448
|
0.0000000
|
157
|
0.0000000
|
0.0000007
|
5
|
|
1
|
26233403
|
26233623
|
0.0000000
|
220
|
0.0000001
|
0.0000554
|
8
|
|
6
|
1624385
|
1624442
|
0.0000001
|
57
|
0.0000001
|
0.0004341
|
2
|
|
5
|
23507449
|
23507656
|
0.0000001
|
207
|
0.0000001
|
0.0001299
|
5
|
|
11
|
73357094
|
73357276
|
0.0000022
|
182
|
0.0000025
|
0.0046583
|
6
|
|
5
|
132113754
|
132113860
|
0.0159548
|
106
|
0.0159548
|
1.0000000
|
3
|
knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Cd_F/Cd_log2_QQ_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Cd_F/Cd_log2_volcano_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Cd_F/Cd_log2_manhattan_DMP_adj.png")

Cd, male
DMP_Cd_M = run_EWAS(DNAm = ComBat.Mvalues.Metals, pheno = pDatAge7Metal_M, var = 'Cd_log2', covar = c('race_child2', 'age_yrs_7y_blood', 'age_mom_enroll_d', 'bmi_mom_prepreg_d', 'coll_grad', 'nullip', 'gt70k', 'smk_preg', 'Bcell_S_7y', 'CD4T_S_7y', 'CD8T_S_7y', 'Neu_S_7y', 'Mono_S_7y', 'NK_S_7y'), anno = anno, path = '/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Cd_M')
# Unadjusted, N = 175
# Unadjusted, p<0.05: 16666
# Unadjusted, FDR<0.05: 0
# Unadjusted, pBonf<0.05: 0
# Adjusted, N = 175
# Adjusted, p<0.05: 19722
# Adjusted, FDR<0.05: 0
# Adjusted, pBonf<0.05: 0
# Adjusted, lambda: 1.070021
# Number of DMRs identified: 3
# rm(DMP_Cd_M); gc()
DMRs
|
chr
|
start
|
end
|
p
|
length
|
fdr
|
sidak
|
nprobe
|
|
20
|
61446961
|
61447369
|
0.00e+00
|
408
|
0.00e+00
|
0.0000000
|
11
|
|
7
|
50518572
|
50518647
|
1.70e-06
|
75
|
2.60e-06
|
0.0090132
|
2
|
|
6
|
28446839
|
28447087
|
5.55e-05
|
248
|
5.55e-05
|
0.0844649
|
2
|
knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Cd_M/Cd_log2_QQ_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Cd_M/Cd_log2_volcano_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Cd_M/Cd_log2_manhattan_DMP_adj.png")

Cr
DMP_Cr = run_EWAS(DNAm = ComBat.Mvalues.Metals, pheno = pDatAge7Metal, var = 'Cr_log2', covar = c('female_d', 'race_child2', 'age_yrs_7y_blood', 'age_mom_enroll_d', 'bmi_mom_prepreg_d', 'coll_grad', 'nullip', 'gt70k', 'smk_preg', 'Bcell_S_7y', 'CD4T_S_7y', 'CD8T_S_7y', 'Neu_S_7y', 'Mono_S_7y', 'NK_S_7y'), anno = anno, path = '/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Cr')
# Unadjusted, N = 333
# Unadjusted, p<0.05: 29723
# Unadjusted, FDR<0.05: 0
# Unadjusted, pBonf<0.05: 0
# Adjusted, N = 333
# Adjusted, p<0.05: 23497
# Adjusted, FDR<0.05: 0
# Adjusted, pBonf<0.05: 0
# Adjusted, lambda: 1.107048
# Number of DMRs identified: 5
# rm(DMP_Cr); gc()
DMRs
|
chr
|
start
|
end
|
p
|
length
|
fdr
|
sidak
|
nprobe
|
|
5
|
145758709
|
145758881
|
0.00e+00
|
172
|
1.00e-07
|
0.0000526
|
4
|
|
16
|
66969473
|
66969500
|
0.00e+00
|
27
|
1.00e-07
|
0.0003537
|
2
|
|
6
|
33245769
|
33245895
|
8.00e-07
|
126
|
1.40e-06
|
0.0025854
|
6
|
|
19
|
50666378
|
50666538
|
1.65e-05
|
160
|
2.07e-05
|
0.0399617
|
3
|
|
6
|
33280198
|
33280228
|
2.17e-05
|
30
|
2.17e-05
|
0.2481969
|
3
|
No adjustment for fish consumption
knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Cr/Cr_log2_QQ_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Cr/Cr_log2_volcano_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Cr/Cr_log2_manhattan_DMP_adj.png")

Cr, female
DMP_Cr_F = run_EWAS(DNAm = ComBat.Mvalues.Metals, pheno = pDatAge7Metal_F, var = 'Cr_log2', covar = c('race_child2', 'age_yrs_7y_blood', 'age_mom_enroll_d', 'bmi_mom_prepreg_d', 'coll_grad', 'nullip', 'gt70k', 'smk_preg', 'Bcell_S_7y', 'CD4T_S_7y', 'CD8T_S_7y', 'Neu_S_7y', 'Mono_S_7y', 'NK_S_7y'), anno = anno, path = '/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Cr_F')
# Unadjusted, N = 158
# Unadjusted, p<0.05: 26701
# Unadjusted, FDR<0.05: 0
# Unadjusted, pBonf<0.05: 0
# Adjusted, N = 158
# Adjusted, p<0.05: 25525
# Adjusted, FDR<0.05: 0
# Adjusted, pBonf<0.05: 0
# Adjusted, lambda: 1.205679
# Number of identified DMR: 0
# rm(DMP_Cr_F); gc()
knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Cr_F/Cr_log2_QQ_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Cr_F/Cr_log2_volcano_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Cr_F/Cr_log2_manhattan_DMP_adj.png")

Cr, male
DMP_Cr_M = run_EWAS(DNAm = ComBat.Mvalues.Metals, pheno = pDatAge7Metal_M, var = 'Cr_log2', covar = c('race_child2', 'age_yrs_7y_blood', 'age_mom_enroll_d', 'bmi_mom_prepreg_d', 'coll_grad', 'nullip', 'gt70k', 'smk_preg', 'Bcell_S_7y', 'CD4T_S_7y', 'CD8T_S_7y', 'Neu_S_7y', 'Mono_S_7y', 'NK_S_7y'), anno = anno, path = '/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Cr_M')
# Unadjusted, N = 175
# Unadjusted, p<0.05: 17887
# Unadjusted, FDR<0.05: 0
# Unadjusted, pBonf<0.05: 0
# Adjusted, N = 175
# Adjusted, p<0.05: 12255
# Adjusted, FDR<0.05: 0
# Adjusted, pBonf<0.05: 0
# Adjusted, lambda: 0.8668368
# Number of DMRs identified: 1
# rm(DMP_Cr_M); gc()
DMRs
|
chr
|
start
|
end
|
p
|
length
|
fdr
|
sidak
|
nprobe
|
|
17
|
46685291
|
46685448
|
0
|
157
|
0
|
3.4e-06
|
5
|
knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Cr_M/Cr_log2_QQ_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Cr_M/Cr_log2_volcano_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Cr_M/Cr_log2_manhattan_DMP_adj.png")

Cs
DMP_Cs = run_EWAS(DNAm = ComBat.Mvalues.Metals, pheno = pDatAge7Metal, var = 'Cs_log2', covar = c('female_d', 'race_child2', 'age_yrs_7y_blood', 'age_mom_enroll_d', 'bmi_mom_prepreg_d', 'coll_grad', 'nullip', 'gt70k', 'smk_preg', 'Bcell_S_7y', 'CD4T_S_7y', 'CD8T_S_7y', 'Neu_S_7y', 'Mono_S_7y', 'NK_S_7y'), anno = anno, path = '/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Cs')
# Unadjusted, N = 333
# Unadjusted, p<0.05: 16687
# Unadjusted, FDR<0.05: 4
# Unadjusted, pBonf<0.05: 2
# Adjusted, N = 333
# Adjusted, p<0.05: 13041
# Adjusted, FDR<0.05: 0
# Adjusted, pBonf<0.05: 0
# Adjusted, lambda: 0.8278941
# Number of DMRs identified: 6
# rm(DMP_Cs); gc()
DMRs
|
chr
|
start
|
end
|
p
|
length
|
fdr
|
sidak
|
nprobe
|
|
6
|
32847584
|
32847845
|
0.0000000
|
261
|
0.0000000
|
0.0000152
|
14
|
|
6
|
33280051
|
33280228
|
0.0000000
|
177
|
0.0000000
|
0.0000334
|
6
|
|
13
|
47472049
|
47472429
|
0.0000000
|
380
|
0.0000001
|
0.0000285
|
12
|
|
10
|
94820922
|
94821085
|
0.0000001
|
163
|
0.0000001
|
0.0002097
|
6
|
|
1
|
68512776
|
68512928
|
0.0000636
|
152
|
0.0000763
|
0.1521621
|
4
|
|
20
|
57427641
|
57427762
|
0.0010790
|
121
|
0.0010790
|
0.9703825
|
6
|
knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Cs/Cs_log2_QQ_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Cs/Cs_log2_volcano_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Cs/Cs_log2_manhattan_DMP_adj.png")

Cs, female
DMP_Cs_F = run_EWAS(DNAm = ComBat.Mvalues.Metals, pheno = pDatAge7Metal_F, var = 'Cs_log2', covar = c('race_child2', 'age_yrs_7y_blood', 'age_mom_enroll_d', 'bmi_mom_prepreg_d', 'coll_grad', 'nullip', 'gt70k', 'smk_preg', 'Bcell_S_7y', 'CD4T_S_7y', 'CD8T_S_7y', 'Neu_S_7y', 'Mono_S_7y', 'NK_S_7y'), anno = anno, path = '/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Cs_F')
# # Unadjusted, N = 158
# Unadjusted, p<0.05: 25871
# Unadjusted, FDR<0.05: 0
# Unadjusted, pBonf<0.05: 0
# Adjusted, N = 158
# Adjusted, p<0.05: 16221
# Adjusted, FDR<0.05: 0
# Adjusted, pBonf<0.05: 0
# Adjusted, lambda: 0.9629794
# Number of DMRs identified: 3
# rm(DMP_Cs_F); gc()
DMRs
|
chr
|
start
|
end
|
p
|
length
|
fdr
|
sidak
|
nprobe
|
|
1
|
200272111
|
200272215
|
0
|
104
|
0
|
7.60e-06
|
3
|
|
20
|
3145355
|
3145597
|
0
|
242
|
0
|
1.60e-05
|
3
|
|
6
|
29648378
|
29648628
|
0
|
250
|
0
|
1.97e-05
|
8
|
knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Cs_F/Cs_log2_QQ_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Cs_F/Cs_log2_volcano_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Cs_F/Cs_log2_manhattan_DMP_adj.png")

Cs, male
DMP_Cs_M = run_EWAS(DNAm = ComBat.Mvalues.Metals, pheno = pDatAge7Metal_M, var = 'Cs_log2', covar = c('race_child2', 'age_yrs_7y_blood', 'age_mom_enroll_d', 'bmi_mom_prepreg_d', 'coll_grad', 'nullip', 'gt70k', 'smk_preg', 'Bcell_S_7y', 'CD4T_S_7y', 'CD8T_S_7y', 'Neu_S_7y', 'Mono_S_7y', 'NK_S_7y'), anno = anno, path = '/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Cs_M')
# Unadjusted, N = 175
# Unadjusted, p<0.05: 15896
# Unadjusted, FDR<0.05: 0
# Unadjusted, pBonf<0.05: 0
# Adjusted, N = 175
# Adjusted, p<0.05: 13428
# Adjusted, FDR<0.05: 0
# Adjusted, pBonf<0.05: 0
# Adjusted, lambda: 0.853948
# Number of DMRs identified: 2
# rm(DMP_Cs_M); gc()
DMRs
|
chr
|
start
|
end
|
p
|
length
|
fdr
|
sidak
|
nprobe
|
|
20
|
57427442
|
57427942
|
0.0000000
|
500
|
0.0000000
|
0.0000005
|
16
|
|
1
|
68512776
|
68512845
|
0.0026516
|
69
|
0.0026516
|
0.9999997
|
3
|
knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Cs_M/Cs_log2_QQ_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Cs_M/Cs_log2_volcano_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Cs_M/Cs_log2_manhattan_DMP_adj.png")

Cu
DMP_Cu = run_EWAS(DNAm = ComBat.Mvalues.Metals, pheno = pDatAge7Metal, var = 'Cu_log2', covar = c('female_d', 'race_child2', 'age_yrs_7y_blood', 'age_mom_enroll_d', 'bmi_mom_prepreg_d', 'coll_grad', 'nullip', 'gt70k', 'smk_preg', 'Bcell_S_7y', 'CD4T_S_7y', 'CD8T_S_7y', 'Neu_S_7y', 'Mono_S_7y', 'NK_S_7y'), anno = anno, path = '/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Cu')
# Unadjusted, N = 333
# Unadjusted, p<0.05: 10199
# Unadjusted, FDR<0.05: 0
# Unadjusted, pBonf<0.05: 0
# Adjusted, N = 333
# Adjusted, p<0.05: 19996
# Adjusted, FDR<0.05: 29
# Adjusted, pBonf<0.05: 9
# Adjusted, lambda: 1.081714
# Number of DMRs identified: 18
# rm(DMP_Cu); gc()
FDR-significant DMPs
|
|
cpg
|
logFC
|
CI.L
|
CI.R
|
AveExpr
|
t
|
P.Value
|
adj.P.Val
|
B
|
adj.P.Val.bonf
|
std_err
|
chr
|
pos
|
gene
|
end
|
|
1551
|
cg00082497
|
-0.2520409
|
-0.3556952
|
-0.1483866
|
-5.3168403
|
-4.784067
|
2.6e-06
|
0.0359038
|
2.498822
|
1.0000000
|
0.0525407
|
chr1
|
32802133
|
MARCKSL1
|
32802133
|
|
2216
|
cg00116766
|
0.4187686
|
0.2817760
|
0.5557613
|
2.0369340
|
6.014386
|
0.0e+00
|
0.0013375
|
6.661993
|
0.0019672
|
0.0696696
|
chr16
|
9857614
|
GRIN2A;GRIN2A;GRIN2A
|
9857614
|
|
15593
|
cg00908120
|
0.5161498
|
0.3285615
|
0.7037382
|
6.2592960
|
5.413594
|
1.0e-07
|
0.0053672
|
4.536415
|
0.0483052
|
0.0955715
|
chr16
|
72872925
|
ZFHX3;ZFHX3
|
72872925
|
|
36122
|
cg02155957
|
0.3783738
|
0.2317081
|
0.5250394
|
3.2458879
|
5.075841
|
7.0e-07
|
0.0144647
|
3.418015
|
0.2603651
|
0.0746248
|
chr1
|
46930731
|
|
46930731
|
|
66105
|
cg04015129
|
0.6991493
|
0.4380113
|
0.9602872
|
4.2830360
|
5.267633
|
3.0e-07
|
0.0077753
|
4.046096
|
0.1010794
|
0.1331776
|
chr10
|
1058036
|
GTPBP4
|
1058036
|
|
76780
|
cg04692924
|
-0.4221533
|
-0.5884130
|
-0.2558937
|
-6.6080183
|
-4.995731
|
1.0e-06
|
0.0182608
|
3.161088
|
0.3834770
|
0.0846568
|
chr1
|
161720042
|
DUSP12
|
161720042
|
|
82479
|
cg05051957
|
-0.4539930
|
-0.6266037
|
-0.2813824
|
-5.5960973
|
-5.174845
|
4.0e-07
|
0.0103119
|
3.739885
|
0.1603134
|
0.0879075
|
chr8
|
141522459
|
CHRAC1;CHRAC1
|
141522459
|
|
96056
|
cg05955013
|
-0.3954311
|
-0.5455648
|
-0.2452975
|
-6.2800794
|
-5.182132
|
4.0e-07
|
0.0103119
|
3.763782
|
0.1546451
|
0.0763997
|
chr17
|
45056646
|
RPRML
|
45056646
|
|
107200
|
cg06723863
|
-0.2584074
|
-0.3627173
|
-0.1540976
|
-5.9821329
|
-4.874088
|
1.7e-06
|
0.0262890
|
2.777821
|
0.6835148
|
0.0528782
|
chr16
|
68270129
|
ESRP2;ESRP2
|
68270129
|
|
117957
|
cg07380021
|
-0.5074974
|
-0.6911466
|
-0.3238481
|
-5.4168894
|
-5.437012
|
1.0e-07
|
0.0053558
|
4.616053
|
0.0428465
|
0.0935562
|
chr1
|
206755252
|
RASSF5;RASSF5;RASSF5
|
206755252
|
|
124637
|
cg07831553
|
0.6064739
|
0.3579392
|
0.8550087
|
3.3703905
|
4.801100
|
2.4e-06
|
0.0343734
|
2.550888
|
0.9624563
|
0.1267359
|
chr19
|
48796974
|
|
48796974
|
|
132730
|
cg08370347
|
0.5104082
|
0.3050049
|
0.7158114
|
3.9077562
|
4.889066
|
1.6e-06
|
0.0254900
|
2.824231
|
0.6372491
|
0.1046840
|
chr5
|
171571793
|
STK10
|
171571793
|
|
157990
|
cg10145926
|
0.6116469
|
0.3869329
|
0.8363609
|
5.3066802
|
5.355331
|
2.0e-07
|
0.0059077
|
4.339440
|
0.0649842
|
0.1145586
|
chr14
|
95875792
|
C14orf139
|
95875792
|
|
165306
|
cg10653573
|
0.8216430
|
0.4935682
|
1.1497177
|
5.4323036
|
4.927492
|
1.3e-06
|
0.0241467
|
2.944904
|
0.5312281
|
0.1673806
|
chr8
|
141347297
|
TRAPPC9;TRAPPC9
|
141347297
|
|
168880
|
cg10923018
|
0.2400925
|
0.1567575
|
0.3234276
|
2.7547510
|
5.668452
|
0.0e+00
|
0.0025621
|
5.418042
|
0.0128106
|
0.0420591
|
chr6
|
31743769
|
C6orf27
|
31743769
|
|
178008
|
cg11608893
|
0.6111347
|
0.3655771
|
0.8566923
|
6.0473017
|
4.896652
|
1.6e-06
|
0.0254900
|
2.847992
|
0.6148187
|
0.1252142
|
chr6
|
32059542
|
TNXB
|
32059542
|
|
184513
|
cg12067421
|
-0.4638647
|
-0.6195019
|
-0.3082274
|
2.0086375
|
-5.863991
|
0.0e+00
|
0.0014972
|
6.113861
|
0.0044916
|
0.0792183
|
chr1
|
203246482
|
|
203246482
|
|
202444
|
cg13434714
|
-0.4198573
|
-0.5838480
|
-0.2558666
|
-5.7702697
|
-5.037302
|
8.0e-07
|
0.0165199
|
3.293966
|
0.3138780
|
0.0834953
|
chr12
|
6936787
|
LEPREL2
|
6936787
|
|
238372
|
cg15790767
|
1.0460317
|
0.6730623
|
1.4190011
|
3.8395189
|
5.518071
|
1.0e-07
|
0.0040292
|
4.893762
|
0.0282044
|
0.1903147
|
chr6
|
13431216
|
GFOD1
|
13431216
|
|
257054
|
cg17143270
|
0.8262133
|
0.5117283
|
1.1406983
|
5.7439128
|
5.169016
|
4.0e-07
|
0.0103119
|
3.720792
|
0.1649911
|
0.1604376
|
chr1
|
91532819
|
|
91532819
|
|
272331
|
cg18299835
|
-0.2325838
|
-0.3271320
|
-0.1380356
|
-4.1342108
|
-4.839937
|
2.0e-06
|
0.0297198
|
2.671477
|
0.8024340
|
0.0478488
|
chr19
|
13207445
|
NFIX
|
13207445
|
|
277756
|
cg18714712
|
-0.5396013
|
-0.7177693
|
-0.3614334
|
-5.9732941
|
-5.958802
|
0.0e+00
|
0.0013375
|
6.457915
|
0.0026750
|
0.0907515
|
chr19
|
49866917
|
DKKL1;TEAD2
|
49866917
|
|
288096
|
cg19532212
|
0.4901147
|
0.3073681
|
0.6728612
|
4.4622674
|
5.276722
|
2.0e-07
|
0.0077753
|
4.076321
|
0.0965815
|
0.0930943
|
chr17
|
56769430
|
TEX14;RAD51C;TEX14;RAD51C
|
56769430
|
|
292461
|
cg19842134
|
-0.2877291
|
-0.4005045
|
-0.1749537
|
-3.5252232
|
-5.019759
|
9.0e-07
|
0.0170704
|
3.238255
|
0.3414082
|
0.0572337
|
chr12
|
54070591
|
ATP5G2;ATP5G2
|
54070591
|
|
299106
|
cg20365618
|
-0.2427541
|
-0.3400297
|
-0.1454786
|
0.4203879
|
-4.909944
|
1.5e-06
|
0.0250879
|
2.890132
|
0.5770213
|
0.0492549
|
chr10
|
121578384
|
INPP5F;INPP5F
|
121578384
|
|
338217
|
cg23477849
|
0.2847709
|
0.1875717
|
0.3819701
|
4.8779575
|
5.764299
|
0.0e+00
|
0.0019215
|
5.757320
|
0.0076859
|
0.0492155
|
chr19
|
5698492
|
LONP1
|
5698492
|
|
370410
|
cg25954729
|
-0.2214209
|
-0.3023661
|
-0.1404758
|
-6.3449744
|
-5.381973
|
1.0e-07
|
0.0056715
|
4.429925
|
0.0567155
|
0.0408229
|
chr11
|
66610784
|
RCE1;C11orf80;RCE1
|
66610784
|
|
381104
|
cg26708724
|
0.6610798
|
0.4075131
|
0.9146465
|
6.7325633
|
5.129526
|
5.0e-07
|
0.0117853
|
3.591901
|
0.2003502
|
0.1293079
|
chr4
|
187509785
|
FAT1
|
187509785
|
|
393045
|
cg27565067
|
0.4808885
|
0.3122348
|
0.6495422
|
6.2036309
|
5.610017
|
0.0e+00
|
0.0029086
|
5.212584
|
0.0174516
|
0.0858822
|
chr17
|
149484
|
RPH3AL
|
149484
|
DMRs
|
chr
|
start
|
end
|
p
|
length
|
fdr
|
sidak
|
nprobe
|
|
22
|
45704901
|
45705265
|
0.0e+00
|
364
|
0.0e+00
|
0.0000000
|
7
|
|
20
|
35169538
|
35169886
|
0.0e+00
|
348
|
0.0e+00
|
0.0000000
|
6
|
|
16
|
66304366
|
66304585
|
0.0e+00
|
219
|
0.0e+00
|
0.0000001
|
3
|
|
10
|
121578136
|
121578639
|
0.0e+00
|
503
|
0.0e+00
|
0.0000001
|
4
|
|
12
|
54070516
|
54070610
|
0.0e+00
|
94
|
0.0e+00
|
0.0000006
|
5
|
|
16
|
8806530
|
8806756
|
0.0e+00
|
226
|
0.0e+00
|
0.0000005
|
7
|
|
17
|
149483
|
149488
|
0.0e+00
|
5
|
0.0e+00
|
0.0001478
|
2
|
|
6
|
1604012
|
1604212
|
0.0e+00
|
200
|
0.0e+00
|
0.0000156
|
5
|
|
20
|
3052114
|
3052483
|
0.0e+00
|
369
|
0.0e+00
|
0.0000175
|
9
|
|
17
|
1395863
|
1396123
|
0.0e+00
|
260
|
0.0e+00
|
0.0000380
|
5
|
|
19
|
55660590
|
55660625
|
0.0e+00
|
35
|
0.0e+00
|
0.0002927
|
4
|
|
15
|
100048370
|
100048500
|
0.0e+00
|
130
|
0.0e+00
|
0.0000987
|
3
|
|
2
|
130345204
|
130345405
|
0.0e+00
|
201
|
1.0e-07
|
0.0000951
|
3
|
|
17
|
47091977
|
47092178
|
1.0e-07
|
201
|
1.0e-07
|
0.0001346
|
4
|
|
19
|
50194119
|
50194252
|
1.0e-07
|
133
|
1.0e-07
|
0.0002220
|
5
|
|
13
|
100310161
|
100310405
|
1.0e-07
|
244
|
1.0e-07
|
0.0001692
|
4
|
|
11
|
19736149
|
19736333
|
1.0e-07
|
184
|
1.0e-07
|
0.0002958
|
5
|
|
1
|
207082827
|
207082900
|
1.1e-06
|
73
|
1.1e-06
|
0.0057588
|
2
|
knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Cu/Cu_log2_QQ_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Cu/Cu_log2_volcano_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Cu/Cu_log2_manhattan_DMP_adj.png")

Cu, female
DMP_Cu_F = run_EWAS(DNAm = ComBat.Mvalues.Metals, pheno = pDatAge7Metal_F, var = 'Cu_log2', covar = c('race_child2', 'age_yrs_7y_blood', 'age_mom_enroll_d', 'bmi_mom_prepreg_d', 'coll_grad', 'nullip', 'gt70k', 'smk_preg', 'Bcell_S_7y', 'CD4T_S_7y', 'CD8T_S_7y', 'Neu_S_7y', 'Mono_S_7y', 'NK_S_7y'), anno = anno, path = '/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Cu_F')
# Unadjusted, N = 158
# Unadjusted, p<0.05: 19233
# Unadjusted, FDR<0.05: 0
# Unadjusted, pBonf<0.05: 0
# Adjusted, N = 158
# Adjusted, p<0.05: 16206
# Adjusted, FDR<0.05: 0
# Adjusted, pBonf<0.05: 0
# Adjusted, lambda: 0.9568499
# Number of DMRs identified: 11
# rm(DMP_Cu_F); gc()
DMRs
|
chr
|
start
|
end
|
p
|
length
|
fdr
|
sidak
|
nprobe
|
|
5
|
191295
|
191806
|
0.0000000
|
511
|
0.0000000
|
0.0000000
|
9
|
|
6
|
32063990
|
32064810
|
0.0000000
|
820
|
0.0000000
|
0.0000000
|
30
|
|
15
|
81426346
|
81426610
|
0.0000000
|
264
|
0.0000000
|
0.0000002
|
7
|
|
11
|
73357094
|
73357396
|
0.0000000
|
302
|
0.0000001
|
0.0000436
|
7
|
|
2
|
74875226
|
74875536
|
0.0000001
|
310
|
0.0000001
|
0.0000721
|
7
|
|
1
|
120174148
|
120174361
|
0.0000001
|
213
|
0.0000002
|
0.0002162
|
2
|
|
17
|
1395863
|
1396123
|
0.0000001
|
260
|
0.0000002
|
0.0002000
|
5
|
|
21
|
37442288
|
37442476
|
0.0000001
|
188
|
0.0000002
|
0.0002909
|
3
|
|
8
|
95962351
|
95962383
|
0.0000021
|
32
|
0.0000025
|
0.0252792
|
4
|
|
19
|
23941312
|
23941438
|
0.0001150
|
126
|
0.0001265
|
0.3023269
|
3
|
|
6
|
31734291
|
31734401
|
0.0008058
|
110
|
0.0008058
|
0.9444595
|
3
|
knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Cu_F/Cu_log2_QQ_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Cu_F/Cu_log2_volcano_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Cu_F/Cu_log2_manhattan_DMP_adj.png")

Cu, male
DMP_Cu_M = run_EWAS(DNAm = ComBat.Mvalues.Metals, pheno = pDatAge7Metal_M, var = 'Cu_log2', covar = c('race_child2', 'age_yrs_7y_blood', 'age_mom_enroll_d', 'bmi_mom_prepreg_d', 'coll_grad', 'nullip', 'gt70k', 'smk_preg', 'Bcell_S_7y', 'CD4T_S_7y', 'CD8T_S_7y', 'Neu_S_7y', 'Mono_S_7y', 'NK_S_7y'), anno = anno, path = '/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Cu_M')
# Unadjusted, N = 175
# Unadjusted, p<0.05: 8255
# Unadjusted, FDR<0.05: 32
# Unadjusted, pBonf<0.05: 5
# Adjusted, N = 175
# Adjusted, p<0.05: 11955
# Adjusted, FDR<0.05: 43
# Adjusted, pBonf<0.05: 13
# Adjusted, lambda: 0.732688
# Number of DMRs identified: 13
# rm(DMP_Cu_M); gc()
FDR-significant DMPs
|
|
cpg
|
logFC
|
CI.L
|
CI.R
|
AveExpr
|
t
|
P.Value
|
adj.P.Val
|
B
|
adj.P.Val.bonf
|
std_err
|
chr
|
pos
|
gene
|
end
|
|
15593
|
cg00908120
|
0.6968301
|
0.4462335
|
0.9474266
|
6.2892750
|
5.491907
|
2.0e-07
|
0.0043618
|
3.025092
|
0.0610657
|
0.1275144
|
chr16
|
72872925
|
ZFHX3;ZFHX3
|
72872925
|
|
17338
|
cg01007589
|
0.9199500
|
0.5976038
|
1.2422962
|
4.7896683
|
5.636547
|
1.0e-07
|
0.0027740
|
3.404180
|
0.0305142
|
0.1642702
|
chr19
|
49894178
|
CCDC155
|
49894178
|
|
18335
|
cg01063965
|
-0.2697333
|
-0.3700510
|
-0.1694156
|
-6.4353826
|
-5.310319
|
4.0e-07
|
0.0095478
|
2.558610
|
0.1432177
|
0.0499143
|
chr11
|
695461
|
TMEM80;TMEM80;DEAF1;DEAF1
|
695461
|
|
24635
|
cg01447660
|
0.3857890
|
0.2320438
|
0.5395341
|
-0.9207246
|
4.955781
|
1.8e-06
|
0.0211997
|
1.670256
|
0.7207908
|
0.0777249
|
chr2
|
69152678
|
|
69152678
|
|
25210
|
cg01485439
|
0.5040485
|
0.3119450
|
0.6961521
|
3.6452587
|
5.182127
|
7.0e-07
|
0.0123633
|
2.231633
|
0.2596284
|
0.0974910
|
chr11
|
67225937
|
CABP4
|
67225937
|
|
36122
|
cg02155957
|
0.4849601
|
0.2932852
|
0.6766350
|
3.2214886
|
4.997028
|
1.5e-06
|
0.0198854
|
1.770337
|
0.6006643
|
0.0972710
|
chr1
|
46930731
|
|
46930731
|
|
41497
|
cg02490920
|
0.3674539
|
0.2288810
|
0.5060267
|
1.3358885
|
5.237070
|
5.0e-07
|
0.0105880
|
2.372126
|
0.2011721
|
0.0698665
|
chr3
|
50304406
|
SEMA3B;SEMA3B
|
50304406
|
|
49479
|
cg02968175
|
0.3051401
|
0.1909359
|
0.4193442
|
5.7555141
|
5.276926
|
4.0e-07
|
0.0098398
|
2.473410
|
0.1672768
|
0.0571880
|
chr16
|
4690020
|
MGRN1;MGRN1;MGRN1;MGRN1
|
4690020
|
|
61452
|
cg03717239
|
0.2988200
|
0.1782864
|
0.4193536
|
0.5057733
|
4.896268
|
2.4e-06
|
0.0247759
|
1.524790
|
0.9385842
|
0.0604897
|
chr8
|
145574318
|
|
145574318
|
|
66105
|
cg04015129
|
0.8389384
|
0.5547224
|
1.1231543
|
4.2710633
|
5.829792
|
0.0e+00
|
0.0013191
|
3.918551
|
0.0118723
|
0.1447437
|
chr10
|
1058036
|
GTPBP4
|
1058036
|
|
72385
|
cg04406071
|
-0.2980754
|
-0.4100451
|
-0.1861057
|
-6.0707229
|
-5.257620
|
5.0e-07
|
0.0101631
|
2.424293
|
0.1829363
|
0.0560206
|
chr17
|
59489784
|
C17orf82
|
59489784
|
|
76780
|
cg04692924
|
-0.5914287
|
-0.8226470
|
-0.3602104
|
-6.5844679
|
-5.051864
|
1.2e-06
|
0.0187815
|
1.905864
|
0.4695367
|
0.1175757
|
chr1
|
161720042
|
DUSP12
|
161720042
|
|
82479
|
cg05051957
|
-0.6067193
|
-0.8484554
|
-0.3649831
|
-5.6069817
|
-4.956986
|
1.8e-06
|
0.0211997
|
1.671792
|
0.7183584
|
0.1229709
|
chr8
|
141522459
|
CHRAC1;CHRAC1
|
141522459
|
|
96056
|
cg05955013
|
-0.4736694
|
-0.6647461
|
-0.2825927
|
-6.2968923
|
-4.895966
|
2.4e-06
|
0.0247759
|
1.522807
|
0.9414854
|
0.0969641
|
chr17
|
45056646
|
RPRML
|
45056646
|
|
117957
|
cg07380021
|
-0.6727208
|
-0.8917216
|
-0.4537201
|
-5.4253082
|
-6.066814
|
0.0e+00
|
0.0010386
|
4.560897
|
0.0036354
|
0.1113060
|
chr1
|
206755252
|
RASSF5;RASSF5;RASSF5
|
206755252
|
|
132177
|
cg08329655
|
-0.4301609
|
-0.5996488
|
-0.2606731
|
-5.8759956
|
-5.012548
|
1.4e-06
|
0.0198854
|
1.809564
|
0.5595710
|
0.0858576
|
chr11
|
7534677
|
PPFIBP2
|
7534677
|
|
133940
|
cg08459368
|
0.5800924
|
0.3505524
|
0.8096324
|
2.7047867
|
4.991261
|
1.6e-06
|
0.0198854
|
1.756039
|
0.6164462
|
0.1167147
|
chr11
|
61974948
|
SCGB2A1
|
61974948
|
|
138326
|
cg08760128
|
0.3023438
|
0.1838403
|
0.4208473
|
6.7313293
|
5.038874
|
1.3e-06
|
0.0191075
|
1.875166
|
0.4967943
|
0.0594315
|
chr16
|
4723507
|
MGRN1;MGRN1;MGRN1;MGRN1
|
4723507
|
|
159790
|
cg10266648
|
1.0455372
|
0.6777917
|
1.4132828
|
5.9758418
|
5.615177
|
1.0e-07
|
0.0028193
|
3.347846
|
0.0338314
|
0.1875055
|
chr2
|
106560529
|
|
106560529
|
|
168880
|
cg10923018
|
0.3493522
|
0.2386925
|
0.4600120
|
2.7253233
|
6.235017
|
0.0e+00
|
0.0007687
|
5.027037
|
0.0015374
|
0.0553357
|
chr6
|
31743769
|
C6orf27
|
31743769
|
|
178008
|
cg11608893
|
0.9384948
|
0.6293671
|
1.2476226
|
6.0805801
|
5.996051
|
0.0e+00
|
0.0010386
|
4.367865
|
0.0051911
|
0.1575025
|
chr6
|
32059542
|
TNXB
|
32059542
|
|
202444
|
cg13434714
|
-0.6677598
|
-0.8632470
|
-0.4722727
|
-5.7834106
|
-6.746422
|
0.0e+00
|
0.0001057
|
6.462646
|
0.0001057
|
0.0992288
|
chr12
|
6936787
|
LEPREL2
|
6936787
|
|
211983
|
cg13989834
|
0.5445790
|
0.3327048
|
0.7564532
|
3.1425732
|
5.076382
|
1.1e-06
|
0.0175131
|
1.966788
|
0.4203137
|
0.1076471
|
chr9
|
134400392
|
UCK1;UCK1
|
134400392
|
|
232975
|
cg15389183
|
-0.2174854
|
-0.3060013
|
-0.1289694
|
-6.1941560
|
-4.852574
|
2.9e-06
|
0.0291746
|
1.418688
|
1.0000000
|
0.0436880
|
chr14
|
102829482
|
TECPR2;CINP
|
102829482
|
|
238372
|
cg15790767
|
1.1582593
|
0.6788697
|
1.6376489
|
3.8648959
|
4.771870
|
4.1e-06
|
0.0386055
|
1.223075
|
1.0000000
|
0.2446072
|
chr6
|
13431216
|
GFOD1
|
13431216
|
|
242146
|
cg16068812
|
-1.0140695
|
-1.4211959
|
-0.6069431
|
-4.2669662
|
-4.919374
|
2.2e-06
|
0.0241887
|
1.579759
|
0.8489923
|
0.2076521
|
chr21
|
44528396
|
U2AF1;U2AF1;U2AF1
|
44528396
|
|
248112
|
cg16496814
|
0.2786227
|
0.1688097
|
0.3884356
|
5.2206210
|
5.011024
|
1.4e-06
|
0.0198854
|
1.806255
|
0.5630518
|
0.0548928
|
chr11
|
9778721
|
|
9778721
|
|
250632
|
cg16656826
|
0.3287551
|
0.2038843
|
0.4536259
|
0.1436170
|
5.199664
|
6.0e-07
|
0.0119506
|
2.277470
|
0.2390116
|
0.0627483
|
chr5
|
159343871
|
ADRA1B;ADRA1B
|
159343871
|
|
277216
|
cg18670846
|
0.7273051
|
0.4270507
|
1.0275594
|
-2.3046149
|
4.784083
|
3.9e-06
|
0.0382303
|
1.252345
|
1.0000000
|
0.1529585
|
chr2
|
68917482
|
|
68917482
|
|
277756
|
cg18714712
|
-0.7278273
|
-0.9713903
|
-0.4842644
|
-5.9498636
|
-5.901856
|
0.0e+00
|
0.0010386
|
4.112559
|
0.0083088
|
0.1239078
|
chr19
|
49866917
|
DKKL1;TEAD2
|
49866917
|
|
281545
|
cg19005275
|
0.6770397
|
0.4430316
|
0.9110478
|
4.2897154
|
5.714189
|
1.0e-07
|
0.0020931
|
3.609791
|
0.0209309
|
0.1190070
|
chr12
|
113588263
|
CCDC42B
|
113588263
|
|
288096
|
cg19532212
|
0.6853542
|
0.4290550
|
0.9416534
|
4.4209486
|
5.281281
|
4.0e-07
|
0.0098398
|
2.482710
|
0.1643357
|
0.1304380
|
chr17
|
56769430
|
TEX14;RAD51C;TEX14;RAD51C
|
56769430
|
|
299106
|
cg20365618
|
-0.3482548
|
-0.4639507
|
-0.2325589
|
0.4046566
|
-5.944876
|
0.0e+00
|
0.0010386
|
4.231669
|
0.0066813
|
0.0579668
|
chr10
|
121578384
|
INPP5F;INPP5F
|
121578384
|
|
301945
|
cg20597842
|
0.9761061
|
0.5701079
|
1.3821044
|
5.8802068
|
4.748367
|
4.6e-06
|
0.0417512
|
1.166880
|
1.0000000
|
0.2070751
|
chr12
|
7818585
|
APOBEC1
|
7818585
|
|
311691
|
cg21373263
|
0.7831825
|
0.4817236
|
1.0846414
|
3.2926911
|
5.131051
|
8.0e-07
|
0.0149060
|
2.103265
|
0.3279323
|
0.1535754
|
chr10
|
126751982
|
CTBP2;CTBP2
|
126751982
|
|
317735
|
cg21864868
|
0.6556443
|
0.4008014
|
0.9104871
|
4.2151756
|
5.081211
|
1.0e-06
|
0.0175131
|
1.978806
|
0.4112293
|
0.1296914
|
chr17
|
46673002
|
LOC404266;LOC404266;LOC404266;LOC404266;LOC404266
|
46673002
|
|
322216
|
cg22240394
|
1.0541992
|
0.6343256
|
1.4740728
|
6.8239404
|
4.958788
|
1.8e-06
|
0.0211997
|
1.676215
|
0.7126127
|
0.2141721
|
chr3
|
186211630
|
|
186211630
|
|
322745
|
cg22286640
|
-0.7778819
|
-1.0993127
|
-0.4564511
|
-4.6467158
|
-4.779666
|
4.0e-06
|
0.0382303
|
1.241753
|
1.0000000
|
0.1638016
|
chr8
|
67026828
|
|
67026828
|
|
336099
|
cg23312431
|
0.3344962
|
0.2000374
|
0.4689549
|
-0.3693187
|
4.913215
|
2.2e-06
|
0.0241887
|
1.566102
|
0.8707948
|
0.0677317
|
chr21
|
45773997
|
TRPM2
|
45773997
|
|
338217
|
cg23477849
|
0.3799812
|
0.2454369
|
0.5145256
|
4.8962493
|
5.577768
|
1.0e-07
|
0.0031066
|
3.251684
|
0.0403856
|
0.0677761
|
chr19
|
5698492
|
LONP1
|
5698492
|
|
352329
|
cg24543538
|
0.8446393
|
0.5105801
|
1.1786986
|
3.2168166
|
4.993663
|
1.5e-06
|
0.0198854
|
1.761957
|
0.6098552
|
0.1702661
|
chr2
|
241569846
|
GPR35
|
241569846
|
|
370410
|
cg25954729
|
-0.3031186
|
-0.4042129
|
-0.2020244
|
-6.3724574
|
-5.921746
|
0.0e+00
|
0.0010386
|
4.169016
|
0.0074984
|
0.0503223
|
chr11
|
66610784
|
RCE1;C11orf80;RCE1
|
66610784
|
|
381104
|
cg26708724
|
0.9627258
|
0.6436003
|
1.2818513
|
6.7173655
|
5.958165
|
0.0e+00
|
0.0010386
|
4.264949
|
0.0062755
|
0.1626214
|
chr4
|
187509785
|
FAT1
|
187509785
|
DMRs
|
chr
|
start
|
end
|
p
|
length
|
fdr
|
sidak
|
nprobe
|
|
10
|
121578136
|
121578846
|
0.0000000
|
710
|
0.0000000
|
0.0000000
|
5
|
|
22
|
45704901
|
45705265
|
0.0000000
|
364
|
0.0000000
|
0.0000000
|
7
|
|
21
|
45773781
|
45773997
|
0.0000000
|
216
|
0.0000000
|
0.0000015
|
2
|
|
4
|
24796918
|
24797176
|
0.0000000
|
258
|
0.0000000
|
0.0000032
|
6
|
|
19
|
50194119
|
50194252
|
0.0000000
|
133
|
0.0000000
|
0.0000267
|
5
|
|
17
|
70723226
|
70723386
|
0.0000000
|
160
|
0.0000000
|
0.0000317
|
2
|
|
20
|
35169593
|
35169886
|
0.0000000
|
293
|
0.0000001
|
0.0000422
|
5
|
|
14
|
78447480
|
78447640
|
0.0000001
|
160
|
0.0000001
|
0.0001307
|
3
|
|
3
|
16216093
|
16216215
|
0.0000001
|
122
|
0.0000001
|
0.0001905
|
4
|
|
17
|
78549323
|
78549371
|
0.0000001
|
48
|
0.0000001
|
0.0006222
|
3
|
|
17
|
149483
|
149488
|
0.0000001
|
5
|
0.0000001
|
0.0080723
|
2
|
|
12
|
54070516
|
54070591
|
0.0000149
|
75
|
0.0000161
|
0.0752227
|
4
|
|
16
|
8806752
|
8806756
|
0.0029944
|
4
|
0.0029944
|
1.0000000
|
2
|
knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Cu_M/Cu_log2_QQ_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Cu_M/Cu_log2_volcano_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Cu_M/Cu_log2_manhattan_DMP_adj.png")

Hg
DMP_Hg = run_EWAS(DNAm = ComBat.Mvalues.Metals, pheno = pDatAge7Metal, var = 'Hg_log2', covar = c('female_d', 'race_child2', 'age_yrs_7y_blood', 'age_mom_enroll_d', 'bmi_mom_prepreg_d', 'coll_grad', 'nullip', 'gt70k', 'smk_preg', 'Bcell_S_7y', 'CD4T_S_7y', 'CD8T_S_7y', 'Neu_S_7y', 'Mono_S_7y', 'NK_S_7y'), anno = anno, path = '/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Hg')
# Unadjusted, N = 326
# Unadjusted, p<0.05: 37293
# Unadjusted, FDR<0.05: 0
# Unadjusted, pBonf<0.05: 0
# Adjusted, N = 326
# Adjusted, p<0.05: 27145
# Adjusted, FDR<0.05: 0
# Adjusted, pBonf<0.05: 0
# Adjusted, lambda: 1.2206
# Number of DMRs identified: 4
# rm(DMP_Hg); gc()
DMRs
|
chr
|
start
|
end
|
p
|
length
|
fdr
|
sidak
|
nprobe
|
|
17
|
46681110
|
46681401
|
0.0000000
|
291
|
0.0000000
|
0.0000007
|
6
|
|
6
|
31846768
|
31847009
|
0.0000000
|
241
|
0.0000000
|
0.0000093
|
9
|
|
10
|
131843516
|
131843725
|
0.0000022
|
209
|
0.0000030
|
0.0042060
|
3
|
|
3
|
42977952
|
42978026
|
0.0004262
|
74
|
0.0004262
|
0.8969299
|
2
|
knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Hg/Hg_log2_QQ_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Hg/Hg_log2_volcano_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Hg/Hg_log2_manhattan_DMP_adj.png")

Hg, female
DMP_Hg_F = run_EWAS(DNAm = ComBat.Mvalues.Metals, pheno = pDatAge7Metal_F, var = 'Hg_log2', covar = c('race_child2', 'age_yrs_7y_blood', 'age_mom_enroll_d', 'bmi_mom_prepreg_d', 'coll_grad', 'nullip', 'gt70k', 'smk_preg', 'Bcell_S_7y', 'CD4T_S_7y', 'CD8T_S_7y', 'Neu_S_7y', 'Mono_S_7y', 'NK_S_7y'), anno = anno, path = '/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Hg_F')
# Unadjusted, N = 154
# Unadjusted, p<0.05: 35686
# Unadjusted, FDR<0.05: 156
# Unadjusted, pBonf<0.05: 1
# Adjusted, N = 154
# Adjusted, p<0.05: 15067
# Adjusted, FDR<0.05: 0
# Adjusted, pBonf<0.05: 0
# Adjusted, lambda: 0.8813254
# Number of DMRs identified: 3
# rm(DMP_Hg_F); gc()
DMRs
|
chr
|
start
|
end
|
p
|
length
|
fdr
|
sidak
|
nprobe
|
|
12
|
47219625
|
47220092
|
0
|
467
|
0
|
0.00e+00
|
12
|
|
4
|
165877874
|
165878136
|
0
|
262
|
0
|
2.10e-06
|
6
|
|
7
|
27143234
|
27143478
|
0
|
244
|
0
|
2.93e-05
|
7
|
knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Hg_F/Hg_log2_QQ_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Hg_F/Hg_log2_volcano_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Hg_F/Hg_log2_manhattan_DMP_adj.png")

Hg, male
DMP_Hg_M = run_EWAS(DNAm = ComBat.Mvalues.Metals, pheno = pDatAge7Metal_M, var = 'Hg_log2', covar = c('race_child2', 'age_yrs_7y_blood', 'age_mom_enroll_d', 'bmi_mom_prepreg_d', 'coll_grad', 'nullip', 'gt70k', 'smk_preg', 'Bcell_S_7y', 'CD4T_S_7y', 'CD8T_S_7y', 'Neu_S_7y', 'Mono_S_7y', 'NK_S_7y'), anno = anno, path = '/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Hg_M')
# Unadjusted, N = 172
# Unadjusted, p<0.05: 22412
# Unadjusted, FDR<0.05: 0
# Unadjusted, pBonf<0.05: 0
# Adjusted, N = 172
# Adjusted, p<0.05: 24779
# Adjusted, FDR<0.05: 0
# Adjusted, pBonf<0.05: 0
# Adjusted, lambda: 1.2248
# Number of DMRs identified: 7
# rm(DMP_Hg_M); gc()
DMRs
|
chr
|
start
|
end
|
p
|
length
|
fdr
|
sidak
|
nprobe
|
|
6
|
31846768
|
31847009
|
0e+00
|
241
|
0e+00
|
0.0000000
|
9
|
|
11
|
18477152
|
18477534
|
0e+00
|
382
|
0e+00
|
0.0000001
|
7
|
|
11
|
18433499
|
18433887
|
0e+00
|
388
|
0e+00
|
0.0000001
|
5
|
|
5
|
502290
|
502571
|
0e+00
|
281
|
0e+00
|
0.0000015
|
3
|
|
6
|
33282735
|
33283162
|
0e+00
|
427
|
0e+00
|
0.0000011
|
20
|
|
14
|
104690039
|
104690244
|
0e+00
|
205
|
0e+00
|
0.0000132
|
5
|
|
1
|
2345151
|
2345410
|
1e-07
|
259
|
1e-07
|
0.0001903
|
8
|
knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Hg_M/Hg_log2_QQ_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Hg_M/Hg_log2_volcano_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Hg_M/Hg_log2_manhattan_DMP_adj.png")

Mg
DMP_Mg = run_EWAS(DNAm = ComBat.Mvalues.Metals, pheno = pDatAge7Metal, var = 'Mg_log2', covar = c('female_d', 'race_child2', 'age_yrs_7y_blood', 'age_mom_enroll_d', 'bmi_mom_prepreg_d', 'coll_grad', 'nullip', 'gt70k', 'smk_preg', 'Bcell_S_7y', 'CD4T_S_7y', 'CD8T_S_7y', 'Neu_S_7y', 'Mono_S_7y', 'NK_S_7y'), anno = anno, path = '/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Mg')
# Unadjusted, N = 333
# Unadjusted, p<0.05: 18232
# Unadjusted, FDR<0.05: 1
# Unadjusted, pBonf<0.05: 1
# Adjusted, N = 333
# Adjusted, p<0.05: 15989
# Adjusted, FDR<0.05: 0
# Adjusted, pBonf<0.05: 0
# Adjusted, lambda: 0.8804657
# Number of DMRs identified: 4
# rm(DMP_Mg); gc()
DMRs
|
chr
|
start
|
end
|
p
|
length
|
fdr
|
sidak
|
nprobe
|
|
20
|
3051953
|
3052345
|
0.0e+00
|
392
|
0.0e+00
|
0.0000000
|
9
|
|
6
|
31543539
|
31543686
|
0.0e+00
|
147
|
0.0e+00
|
0.0000326
|
8
|
|
2
|
240196768
|
240196996
|
0.0e+00
|
228
|
1.0e-07
|
0.0000792
|
3
|
|
11
|
368564
|
368712
|
1.9e-06
|
148
|
1.9e-06
|
0.0049840
|
7
|
knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Mg/Mg_log2_QQ_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Mg/Mg_log2_volcano_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Mg/Mg_log2_manhattan_DMP_adj.png")

Mg, female
DMP_Mg_F = run_EWAS(DNAm = ComBat.Mvalues.Metals, pheno = pDatAge7Metal_F, var = 'Mg_log2', covar = c('race_child2', 'age_yrs_7y_blood', 'age_mom_enroll_d', 'bmi_mom_prepreg_d', 'coll_grad', 'nullip', 'gt70k', 'smk_preg', 'Bcell_S_7y', 'CD4T_S_7y', 'CD8T_S_7y', 'Neu_S_7y', 'Mono_S_7y', 'NK_S_7y'), anno = anno, path = '/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Mg_F')
# Unadjusted, N = 158
# Unadjusted, p<0.05: 33977
# Unadjusted, FDR<0.05: 0
# Unadjusted, pBonf<0.05: 0
# Adjusted, N = 158
# Adjusted, p<0.05: 20666
# Adjusted, FDR<0.05: 0
# Adjusted, pBonf<0.05: 0
# Adjusted, lambda: 1.081664
# Number of DMRs identified: 2
# rm(DMP_Mg_F); gc()
DMRs
|
chr
|
start
|
end
|
p
|
length
|
fdr
|
sidak
|
nprobe
|
|
2
|
240196876
|
240196996
|
0.0000008
|
120
|
0.0000016
|
0.0025678
|
2
|
|
6
|
10884093
|
10884140
|
0.0002591
|
47
|
0.0002591
|
0.8863834
|
2
|
knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Mg_F/Mg_log2_QQ_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Mg_F/Mg_log2_volcano_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Mg_F/Mg_log2_manhattan_DMP_adj.png")

Mg, male
DMP_Mg_M = run_EWAS(DNAm = ComBat.Mvalues.Metals, pheno = pDatAge7Metal_M, var = 'Mg_log2', covar = c('race_child2', 'age_yrs_7y_blood', 'age_mom_enroll_d', 'bmi_mom_prepreg_d', 'coll_grad', 'nullip', 'gt70k', 'smk_preg', 'Bcell_S_7y', 'CD4T_S_7y', 'CD8T_S_7y', 'Neu_S_7y', 'Mono_S_7y', 'NK_S_7y'), anno = anno, path = '/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Mg_M')
# Unadjusted, N = 175
# Unadjusted, p<0.05: 9395
# Unadjusted, FDR<0.05: 7
# Unadjusted, pBonf<0.05: 5
# Adjusted, N = 175
# Adjusted, p<0.05: 13518
# Adjusted, FDR<0.05: 3
# Adjusted, pBonf<0.05: 3
# Adjusted, lambda: 0.8045591
# Number of identified DMR: 0
# rm(DMP_Mg_M); gc()
DMRs
|
chr
|
start
|
end
|
p
|
length
|
fdr
|
sidak
|
nprobe
|
|
21
|
45773781
|
45773997
|
0.0000000
|
216
|
0.0000000
|
0.0000013
|
2
|
|
17
|
37123637
|
37123949
|
0.0000000
|
312
|
0.0000001
|
0.0000317
|
9
|
|
5
|
23507449
|
23507656
|
0.0000000
|
207
|
0.0000002
|
0.0000915
|
5
|
|
2
|
152830504
|
152830665
|
0.0000001
|
161
|
0.0000003
|
0.0002264
|
5
|
|
17
|
47091977
|
47092178
|
0.0000001
|
201
|
0.0000003
|
0.0002324
|
4
|
|
10
|
121578383
|
121578639
|
0.0000003
|
256
|
0.0000005
|
0.0003992
|
3
|
|
6
|
31543539
|
31543686
|
0.0000004
|
147
|
0.0000006
|
0.0010323
|
8
|
|
3
|
138725152
|
138725425
|
0.0000004
|
273
|
0.0000006
|
0.0006235
|
7
|
|
12
|
54385274
|
54385526
|
0.0000008
|
252
|
0.0000009
|
0.0012112
|
4
|
|
17
|
70723226
|
70723386
|
0.0000013
|
160
|
0.0000014
|
0.0032358
|
2
|
|
11
|
368564
|
368638
|
0.0002279
|
74
|
0.0002279
|
0.7033206
|
5
|
knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Mg_M/Mg_log2_QQ_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Mg_M/Mg_log2_volcano_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Mg_M/Mg_log2_manhattan_DMP_adj.png")

Mn
DMP_Mn = run_EWAS(DNAm = ComBat.Mvalues.Metals, pheno = pDatAge7Metal, var = 'Mn_log2', covar = c('female_d', 'race_child2', 'age_yrs_7y_blood', 'age_mom_enroll_d', 'bmi_mom_prepreg_d', 'coll_grad', 'nullip', 'gt70k', 'smk_preg', 'Bcell_S_7y', 'CD4T_S_7y', 'CD8T_S_7y', 'Neu_S_7y', 'Mono_S_7y', 'NK_S_7y'), anno = anno, path = '/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Mn')
# Unadjusted, N = 333
# Unadjusted, p<0.05: 27983
# Unadjusted, FDR<0.05: 6
# Unadjusted, pBonf<0.05: 1
# Adjusted, N = 333
# Adjusted, p<0.05: 39149
# Adjusted, FDR<0.05: 14
# Adjusted, pBonf<0.05: 3
# Adjusted, lambda: 1.35996
# Number of DMRs identified: 7
# rm(DMP_Mn); gc()
FDR-significant DMPs
|
|
cpg
|
logFC
|
CI.L
|
CI.R
|
AveExpr
|
t
|
P.Value
|
adj.P.Val
|
B
|
adj.P.Val.bonf
|
std_err
|
chr
|
pos
|
gene
|
end
|
|
13985
|
cg00808511
|
0.1797749
|
0.1076657
|
0.2518840
|
2.8599969
|
4.905172
|
1.5e-06
|
0.0441677
|
4.921202
|
0.5905329
|
0.0367425
|
chr16
|
52495237
|
TOX3;TOX3
|
52495237
|
|
61437
|
cg03716590
|
0.1820431
|
0.1108155
|
0.2532707
|
5.0904967
|
5.028534
|
8.0e-07
|
0.0327455
|
5.457274
|
0.3274551
|
0.0362916
|
chr7
|
95435309
|
DYNC1I1;DYNC1I1;DYNC1I1
|
95435309
|
|
90890
|
cg05613017
|
0.1995162
|
0.1227136
|
0.2763187
|
5.3286885
|
5.111142
|
6.0e-07
|
0.0272713
|
5.822518
|
0.2192172
|
0.0391431
|
chr12
|
65589446
|
LEMD3;LEMD3
|
65589446
|
|
153815
|
cg09856068
|
-0.1132155
|
-0.1568602
|
-0.0695708
|
-4.3655995
|
-5.103735
|
6.0e-07
|
0.0272713
|
5.790109
|
0.2271515
|
0.0221605
|
chr5
|
170878246
|
FGF18
|
170878246
|
|
170758
|
cg11063328
|
-0.1609044
|
-0.2222669
|
-0.0995418
|
-6.0173655
|
-5.159174
|
4.0e-07
|
0.0272713
|
6.037176
|
0.1731901
|
0.0312433
|
chr11
|
18343203
|
GTF2H1;HPS5;HPS5;HPS5;GTF2H1
|
18343203
|
|
171438
|
cg11115211
|
-0.1889357
|
-0.2648699
|
-0.1130014
|
-5.8811483
|
-4.895440
|
1.6e-06
|
0.0441677
|
4.879395
|
0.6183473
|
0.0386990
|
chr3
|
67704890
|
SUCLG2
|
67704890
|
|
209344
|
cg13834844
|
-0.1019035
|
-0.1391228
|
-0.0646842
|
-5.1364932
|
-5.386845
|
1.0e-07
|
0.0138315
|
7.077995
|
0.0553259
|
0.0188544
|
chr10
|
102415320
|
|
102415320
|
|
216559
|
cg14252211
|
0.1929530
|
0.1274370
|
0.2584689
|
5.8503162
|
5.794555
|
0.0e+00
|
0.0032695
|
9.031255
|
0.0065390
|
0.0333691
|
chr1
|
25919394
|
|
25919394
|
|
286458
|
cg19407717
|
0.3110043
|
0.2209750
|
0.4010336
|
4.0277865
|
6.796700
|
0.0e+00
|
0.0000211
|
14.301558
|
0.0000211
|
0.0459058
|
chr2
|
1544120
|
TPO;TPO;TPO;TPO
|
1544120
|
|
286677
|
cg19425870
|
-0.1477253
|
-0.2059407
|
-0.0895098
|
-6.4570149
|
-4.992663
|
1.0e-06
|
0.0353787
|
5.300234
|
0.3891653
|
0.0296320
|
chr11
|
3876808
|
STIM1
|
3876808
|
|
326256
|
cg22586726
|
0.2701506
|
0.1619704
|
0.3783308
|
-0.9735686
|
4.913305
|
1.4e-06
|
0.0441677
|
4.956198
|
0.5682174
|
0.0551823
|
chr10
|
134150542
|
LRRC27;LRRC27;LRRC27;LRRC27;LRRC27
|
134150542
|
|
347861
|
cg24196240
|
0.3273967
|
0.2094577
|
0.4453357
|
5.2479144
|
5.461758
|
1.0e-07
|
0.0125768
|
7.427654
|
0.0377305
|
0.0601685
|
chr21
|
36096009
|
NCRNA00160
|
36096009
|
|
359777
|
cg25101184
|
0.2474977
|
0.1517913
|
0.3432040
|
3.3810389
|
5.087987
|
6.0e-07
|
0.0272713
|
5.719635
|
0.2454421
|
0.0488076
|
chr14
|
56231604
|
RPL13AP3
|
56231604
|
|
386595
|
cg27095984
|
-0.1889690
|
-0.2595782
|
-0.1183597
|
5.2710750
|
-5.265561
|
3.0e-07
|
0.0204265
|
6.518590
|
0.1021325
|
0.0359752
|
chr13
|
21652115
|
|
21652115
|
DMRs
|
chr
|
start
|
end
|
p
|
length
|
fdr
|
sidak
|
nprobe
|
|
10
|
134150488
|
134150760
|
0.0000000
|
272
|
0.0000000
|
0.0000000
|
7
|
|
19
|
21657528
|
21657756
|
0.0000000
|
228
|
0.0000000
|
0.0000001
|
4
|
|
16
|
30572738
|
30573013
|
0.0000000
|
275
|
0.0000000
|
0.0000011
|
5
|
|
16
|
73100425
|
73100510
|
0.0000000
|
85
|
0.0000000
|
0.0001111
|
2
|
|
10
|
45406680
|
45406847
|
0.0000000
|
167
|
0.0000000
|
0.0000744
|
3
|
|
20
|
61659979
|
61660250
|
0.0000001
|
271
|
0.0000001
|
0.0000929
|
2
|
|
10
|
35484767
|
35484824
|
0.0002039
|
57
|
0.0002039
|
0.7560663
|
3
|
knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Mn/Mn_log2_QQ_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Mn/Mn_log2_volcano_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Mn/Mn_log2_manhattan_DMP_adj.png")

Mn, female
DMP_Mn_F = run_EWAS(DNAm = ComBat.Mvalues.Metals, pheno = pDatAge7Metal_F, var = 'Mn_log2', covar = c('race_child2', 'age_yrs_7y_blood', 'age_mom_enroll_d', 'bmi_mom_prepreg_d', 'coll_grad', 'nullip', 'gt70k', 'smk_preg', 'Bcell_S_7y', 'CD4T_S_7y', 'CD8T_S_7y', 'Neu_S_7y', 'Mono_S_7y', 'NK_S_7y'), anno = anno, path = '/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Mn_F')
# Unadjusted, N = 158
# Unadjusted, p<0.05: 28256
# Unadjusted, FDR<0.05: 3
# Unadjusted, pBonf<0.05: 3
# Adjusted, N = 158
# Adjusted, p<0.05: 40111
# Adjusted, FDR<0.05: 3
# Adjusted, pBonf<0.05: 3
# Adjusted, lambda: 1.365691
# Number of DMRs identified: 2
# rm(DMP_Mn_F); gc()
FDR-significant DMPs
|
|
cpg
|
logFC
|
CI.L
|
CI.R
|
AveExpr
|
t
|
P.Value
|
adj.P.Val
|
B
|
adj.P.Val.bonf
|
std_err
|
chr
|
pos
|
gene
|
end
|
|
170758
|
cg11063328
|
-0.2542536
|
-0.3311487
|
-0.1773585
|
-6.003312
|
-6.536372
|
0e+00
|
0.0004165
|
11.101209
|
0.0004165
|
0.0390272
|
chr11
|
18343203
|
GTF2H1;HPS5;HPS5;HPS5;GTF2H1
|
18343203
|
|
286677
|
cg19425870
|
-0.2408160
|
-0.3166778
|
-0.1649541
|
-6.446281
|
-6.275239
|
0e+00
|
0.0007852
|
9.941850
|
0.0015705
|
0.0384954
|
chr11
|
3876808
|
STIM1
|
3876808
|
|
324070
|
cg22396353
|
-0.1482285
|
-0.2007424
|
-0.0957146
|
-6.101068
|
-5.579761
|
1e-07
|
0.0154847
|
6.983409
|
0.0464542
|
0.0264223
|
chr22
|
46692687
|
GTSE1;GTSE1;CN5H6.4
|
46692687
|
DMRs
|
chr
|
start
|
end
|
p
|
length
|
fdr
|
sidak
|
nprobe
|
|
6
|
3849380
|
3849702
|
0.0e+00
|
322
|
1.0e-07
|
0.0000351
|
13
|
|
11
|
76839190
|
76839217
|
5.3e-06
|
27
|
5.3e-06
|
0.0742406
|
3
|
knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Mn_F/Mn_log2_QQ_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Mn_F/Mn_log2_volcano_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Mn_F/Mn_log2_manhattan_DMP_adj.png")

Mn, male
DMP_Mn_M = run_EWAS(DNAm = ComBat.Mvalues.Metals, pheno = pDatAge7Metal_M, var = 'Mn_log2', covar = c('race_child2', 'age_yrs_7y_blood', 'age_mom_enroll_d', 'bmi_mom_prepreg_d', 'coll_grad', 'nullip', 'gt70k', 'smk_preg', 'Bcell_S_7y', 'CD4T_S_7y', 'CD8T_S_7y', 'Neu_S_7y', 'Mono_S_7y', 'NK_S_7y'), anno = anno, path = '/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Mn_M')
Unadjusted, N = 175
Unadjusted, p<0.05: 14905
Unadjusted, FDR<0.05: 27
Unadjusted, pBonf<0.05: 9
Adjusted, N = 175
Adjusted, p<0.05: 19138
Adjusted, FDR<0.05: 30
Adjusted, pBonf<0.05: 13
Adjusted, lambda: 0.9881206
Number of DMRs identified: 12
# rm(DMP_Mn_M); gc()
knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Mn_M/Mn_log2_QQ_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Mn_M/Mn_log2_volcano_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Mn_M/Mn_log2_manhattan_DMP_adj.png")

FDR-significant DMPs
|
|
cpg
|
logFC
|
CI.L
|
CI.R
|
AveExpr
|
t
|
P.Value
|
adj.P.Val
|
B
|
adj.P.Val.bonf
|
std_err
|
chr
|
pos
|
gene
|
end
|
|
56695
|
cg03425412
|
-0.2215880
|
-0.3084393
|
-0.1347367
|
-5.940582
|
-5.038959
|
1.3e-06
|
0.0226177
|
4.630103
|
0.4975885
|
0.0440754
|
chr20
|
21500337
|
|
21500337
|
|
68153
|
cg04143120
|
0.4096425
|
0.2732188
|
0.5460663
|
6.792018
|
5.930435
|
0.0e+00
|
0.0010296
|
8.159475
|
0.0072071
|
0.0694995
|
chr11
|
72968848
|
|
72968848
|
|
79809
|
cg04885068
|
0.1877474
|
0.1216510
|
0.2538439
|
6.474553
|
5.609957
|
1.0e-07
|
0.0032325
|
6.851750
|
0.0345882
|
0.0333719
|
chr1
|
9099298
|
SLC2A5;SLC2A5
|
9099298
|
|
82300
|
cg05041382
|
-0.1229809
|
-0.1725540
|
-0.0734078
|
-6.391825
|
-4.899538
|
2.3e-06
|
0.0330400
|
4.114159
|
0.9251202
|
0.0247765
|
chr13
|
50366546
|
KPNA3
|
50366546
|
|
85445
|
cg05249026
|
-0.1644832
|
-0.2257280
|
-0.1032385
|
-2.355604
|
-5.304156
|
4.0e-07
|
0.0081883
|
5.643430
|
0.1473888
|
0.0308565
|
chr16
|
11031524
|
DEXI
|
11031524
|
|
97510
|
cg06051716
|
0.3566344
|
0.2441486
|
0.4691202
|
6.493667
|
6.261770
|
0.0e+00
|
0.0002468
|
9.558316
|
0.0013459
|
0.0572337
|
chr6
|
169225783
|
|
169225783
|
|
107728
|
cg06756211
|
-0.2081794
|
-0.2740447
|
-0.1423141
|
-6.049441
|
-6.242302
|
0.0e+00
|
0.0002468
|
9.478836
|
0.0014809
|
0.0332522
|
chr1
|
223936799
|
CAPN2;CAPN2
|
223936799
|
|
109948
|
cg06883949
|
-0.1214334
|
-0.1679112
|
-0.0749557
|
-6.468868
|
-5.160082
|
7.0e-07
|
0.0143290
|
5.089503
|
0.2865793
|
0.0231544
|
chr4
|
1795240
|
FGFR3;FGFR3;FGFR3
|
1795240
|
|
128092
|
cg08072480
|
-0.1393237
|
-0.1948333
|
-0.0838141
|
-6.612619
|
-4.957019
|
1.8e-06
|
0.0298678
|
4.326339
|
0.7168284
|
0.0278749
|
chr11
|
65292666
|
SCYL1;SCYL1
|
65292666
|
|
157031
|
cg10088075
|
-0.1106800
|
-0.1561537
|
-0.0652063
|
-6.213891
|
-4.806981
|
3.5e-06
|
0.0463062
|
3.776162
|
1.0000000
|
0.0226270
|
chr16
|
30407103
|
ZNF48;ZNF48
|
30407103
|
|
176390
|
cg11480534
|
0.3975879
|
0.2442723
|
0.5509035
|
5.838834
|
5.121748
|
9.0e-07
|
0.0162915
|
4.941954
|
0.3421211
|
0.0781475
|
chr11
|
62255850
|
AHNAK
|
62255850
|
|
176843
|
cg11521780
|
-0.1371987
|
-0.1836223
|
-0.0907750
|
-5.767858
|
-5.836788
|
0.0e+00
|
0.0014287
|
7.775114
|
0.0114294
|
0.0231260
|
chr12
|
53693949
|
C12orf10
|
53693949
|
|
180100
|
cg11755803
|
0.4054795
|
0.2439920
|
0.5669669
|
5.790724
|
4.959083
|
1.8e-06
|
0.0298678
|
4.332328
|
0.7116767
|
0.0823297
|
chr12
|
129000542
|
TMEM132C
|
129000542
|
|
192975
|
cg12700904
|
-0.1026171
|
-0.1442559
|
-0.0609784
|
-5.936497
|
-4.867273
|
2.7e-06
|
0.0367795
|
3.995819
|
1.0000000
|
0.0206063
|
chr3
|
13590720
|
FBLN2;FBLN2
|
13590720
|
|
194538
|
cg12828656
|
-0.1505408
|
-0.1978614
|
-0.1032201
|
-0.497092
|
-6.283003
|
0.0e+00
|
0.0002468
|
9.653365
|
0.0012011
|
0.0235966
|
chr5
|
132577108
|
FSTL4
|
132577108
|
|
209344
|
cg13834844
|
-0.1537219
|
-0.2150872
|
-0.0923565
|
-5.125143
|
-4.947389
|
1.9e-06
|
0.0299292
|
4.290672
|
0.7482293
|
0.0309191
|
chr10
|
102415320
|
|
102415320
|
|
209541
|
cg13848566
|
-0.1657616
|
-0.2254232
|
-0.1061000
|
-6.364105
|
-5.487225
|
2.0e-07
|
0.0041510
|
6.361612
|
0.0622649
|
0.0300344
|
chr9
|
89561175
|
GAS1
|
89561175
|
|
214672
|
cg14149680
|
-0.2933548
|
-0.3823188
|
-0.2043908
|
-6.352664
|
-6.512538
|
0.0e+00
|
0.0001218
|
10.644399
|
0.0003654
|
0.0451606
|
chr11
|
2187632
|
TH;TH;TH
|
2187632
|
|
249118
|
cg16560774
|
-0.1674158
|
-0.2247905
|
-0.1100411
|
-6.459545
|
-5.762880
|
0.0e+00
|
0.0018270
|
7.471818
|
0.0164430
|
0.0288456
|
chr17
|
79373381
|
BAHCC1
|
79373381
|
|
286458
|
cg19407717
|
0.4941274
|
0.3507014
|
0.6375534
|
4.033610
|
6.804284
|
0.0e+00
|
0.0000420
|
11.935137
|
0.0000775
|
0.0730850
|
chr2
|
1544120
|
TPO;TPO;TPO;TPO
|
1544120
|
|
287817
|
cg19511862
|
-0.1036380
|
-0.1427175
|
-0.0645584
|
-6.258253
|
-5.237605
|
5.0e-07
|
0.0105619
|
5.386300
|
0.2006761
|
0.0192509
|
chr12
|
125478458
|
BRI3BP
|
125478458
|
|
289598
|
cg19641404
|
-0.1138848
|
-0.1597132
|
-0.0680564
|
-5.865794
|
-4.907886
|
2.3e-06
|
0.0330400
|
4.144868
|
0.8915828
|
0.0228134
|
chr2
|
232826272
|
DIS3L2
|
232826272
|
|
299702
|
cg20414082
|
0.2602966
|
0.1634793
|
0.3571138
|
3.200594
|
5.309910
|
4.0e-07
|
0.0081883
|
5.663610
|
0.1438533
|
0.0491946
|
chr1
|
203002593
|
|
203002593
|
|
300828
|
cg20504533
|
-0.2169473
|
-0.2800653
|
-0.1538293
|
-5.852235
|
-6.788360
|
0.0e+00
|
0.0000420
|
11.869177
|
0.0000839
|
0.0318283
|
chr17
|
15848253
|
ADORA2B;ADORA2B
|
15848253
|
|
326031
|
cg22563312
|
-0.1654587
|
-0.2241965
|
-0.1067209
|
-6.274307
|
-5.563337
|
1.0e-07
|
0.0033295
|
6.664767
|
0.0432836
|
0.0295544
|
chr5
|
179334739
|
TBC1D9B;TBC1D9B
|
179334739
|
|
327739
|
cg22702772
|
-0.1485121
|
-0.2011945
|
-0.0958296
|
-6.685949
|
-5.567491
|
1.0e-07
|
0.0033295
|
6.681390
|
0.0424292
|
0.0264012
|
chr3
|
48699012
|
CELSR3
|
48699012
|
|
347861
|
cg24196240
|
0.4158514
|
0.2668619
|
0.5648410
|
5.267386
|
5.512565
|
1.0e-07
|
0.0039531
|
6.459776
|
0.0553431
|
0.0759332
|
chr21
|
36096009
|
NCRNA00160
|
36096009
|
|
357841
|
cg24948962
|
-0.2158814
|
-0.2919582
|
-0.1398046
|
-5.437432
|
-5.604397
|
1.0e-07
|
0.0032325
|
6.828678
|
0.0355576
|
0.0385319
|
chr18
|
2906032
|
EMILIN2
|
2906032
|
|
360532
|
cg25152909
|
0.4300346
|
0.2746166
|
0.5854525
|
6.076684
|
5.464792
|
2.0e-07
|
0.0043413
|
6.270370
|
0.0694607
|
0.0792235
|
chr5
|
172566090
|
C5orf41
|
172566090
|
|
364427
|
cg25466588
|
-0.0942618
|
-0.1322555
|
-0.0562681
|
-5.901716
|
-4.899910
|
2.3e-06
|
0.0330400
|
4.115528
|
0.9235979
|
0.0186738
|
chr3
|
23958904
|
NKIRAS1;RPL15
|
23958904
|
DMRs
|
chr
|
start
|
end
|
p
|
length
|
fdr
|
sidak
|
nprobe
|
|
1
|
161008461
|
161008977
|
0.00e+00
|
516
|
0.00e+00
|
0.0000000
|
8
|
|
19
|
21657528
|
21658001
|
0.00e+00
|
473
|
0.00e+00
|
0.0000000
|
5
|
|
19
|
10736005
|
10736117
|
0.00e+00
|
112
|
0.00e+00
|
0.0000053
|
5
|
|
20
|
5485244
|
5485511
|
0.00e+00
|
267
|
0.00e+00
|
0.0000034
|
6
|
|
4
|
79971176
|
79971432
|
0.00e+00
|
256
|
0.00e+00
|
0.0000077
|
4
|
|
20
|
35169593
|
35169886
|
0.00e+00
|
293
|
0.00e+00
|
0.0000076
|
5
|
|
1
|
9099280
|
9099462
|
1.00e-07
|
182
|
1.00e-07
|
0.0001413
|
3
|
|
6
|
26018002
|
26018185
|
1.00e-07
|
183
|
2.00e-07
|
0.0002188
|
6
|
|
3
|
39543966
|
39544192
|
2.90e-06
|
226
|
3.80e-06
|
0.0050183
|
2
|
|
15
|
91473090
|
91473365
|
6.10e-06
|
275
|
7.40e-06
|
0.0087499
|
4
|
|
19
|
12444612
|
12444741
|
9.80e-06
|
129
|
1.06e-05
|
0.0293841
|
5
|
|
6
|
37616597
|
37616686
|
8.58e-05
|
89
|
8.58e-05
|
0.3164878
|
2
|
Pb
DMP_Pb = run_EWAS(DNAm = ComBat.Mvalues.Metals, pheno = pDatAge7Metal, var = 'Pb_log2', covar = c('female_d', 'race_child2', 'age_yrs_7y_blood', 'age_mom_enroll_d', 'bmi_mom_prepreg_d', 'coll_grad', 'nullip', 'gt70k', 'smk_preg', 'Bcell_S_7y', 'CD4T_S_7y', 'CD8T_S_7y', 'Neu_S_7y', 'Mono_S_7y', 'NK_S_7y'), anno = anno, path = '/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Pb')
# # Unadjusted, N = 333
# Unadjusted, p<0.05: 13157
# Unadjusted, FDR<0.05: 0
# Unadjusted, pBonf<0.05: 0
# Adjusted, N = 333
# Adjusted, p<0.05: 19418
# Adjusted, FDR<0.05: 0
# Adjusted, pBonf<0.05: 0
# Adjusted, lambda: 1.040491
# Number of DMRs identified: 8
# rm(DMP_Pb); gc()
DMRs
|
chr
|
start
|
end
|
p
|
length
|
fdr
|
sidak
|
nprobe
|
|
10
|
135051021
|
135051581
|
0.0000000
|
560
|
0.0000000
|
0.0000000
|
11
|
|
22
|
45704901
|
45705265
|
0.0000000
|
364
|
0.0000000
|
0.0000000
|
7
|
|
22
|
19746155
|
19746368
|
0.0000000
|
213
|
0.0000000
|
0.0000309
|
3
|
|
3
|
130745441
|
130745685
|
0.0000000
|
244
|
0.0000001
|
0.0000426
|
10
|
|
7
|
155283139
|
155283424
|
0.0000001
|
285
|
0.0000001
|
0.0001025
|
3
|
|
14
|
104690039
|
104690244
|
0.0000001
|
205
|
0.0000001
|
0.0001464
|
5
|
|
6
|
2891972
|
2892152
|
0.0000001
|
180
|
0.0000001
|
0.0001715
|
5
|
|
1
|
68512776
|
68512845
|
0.0001164
|
69
|
0.0001164
|
0.4859412
|
3
|
knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Pb/Pb_log2_QQ_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Pb/Pb_log2_volcano_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Pb/Pb_log2_manhattan_DMP_adj.png")

Pb, female
DMP_Pb_F = run_EWAS(DNAm = ComBat.Mvalues.Metals, pheno = pDatAge7Metal_F, var = 'Pb_log2', covar = c('race_child2', 'age_yrs_7y_blood', 'age_mom_enroll_d', 'bmi_mom_prepreg_d', 'coll_grad', 'nullip', 'gt70k', 'smk_preg', 'Bcell_S_7y', 'CD4T_S_7y', 'CD8T_S_7y', 'Neu_S_7y', 'Mono_S_7y', 'NK_S_7y'), anno = anno, path = '/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Pb_F')
# Unadjusted, N = 158
# Unadjusted, p<0.05: 10571
# Unadjusted, FDR<0.05: 0
# Unadjusted, pBonf<0.05: 0
# Adjusted, N = 158
# Adjusted, p<0.05: 12301
# Adjusted, FDR<0.05: 0
# Adjusted, pBonf<0.05: 0
# Adjusted, lambda: 0.7551375
# Number of identified DMR: 0
# rm(DMP_Pb_F); gc()
knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Pb_F/Pb_log2_QQ_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Pb_F/Pb_log2_volcano_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Pb_F/Pb_log2_manhattan_DMP_adj.png")

Pb, male
DMP_Pb_M = run_EWAS(DNAm = ComBat.Mvalues.Metals, pheno = pDatAge7Metal_M, var = 'Pb_log2', covar = c('race_child2', 'age_yrs_7y_blood', 'age_mom_enroll_d', 'bmi_mom_prepreg_d', 'coll_grad', 'nullip', 'gt70k', 'smk_preg', 'Bcell_S_7y', 'CD4T_S_7y', 'CD8T_S_7y', 'Neu_S_7y', 'Mono_S_7y', 'NK_S_7y'), anno = anno, path = '/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Pb_M')
# Unadjusted, N = 175
# Unadjusted, p<0.05: 18362
# Unadjusted, FDR<0.05: 0
# Unadjusted, pBonf<0.05: 0
# Adjusted, N = 175
# Adjusted, p<0.05: 12960
# Adjusted, FDR<0.05: 0
# Adjusted, pBonf<0.05: 0
# Adjusted, lambda: 0.8922977
# Number of DMRs identified: 5
# rm(DMP_Pb_M); gc()
DMRs
|
chr
|
start
|
end
|
p
|
length
|
fdr
|
sidak
|
nprobe
|
|
6
|
33084548
|
33084985
|
0.0000000
|
437
|
0.0000000
|
0.0000000
|
12
|
|
1
|
68512649
|
68513063
|
0.0000000
|
414
|
0.0000000
|
0.0000001
|
7
|
|
6
|
31148331
|
31148748
|
0.0000000
|
417
|
0.0000000
|
0.0000008
|
14
|
|
22
|
45704987
|
45705265
|
0.0000001
|
278
|
0.0000001
|
0.0000883
|
5
|
|
19
|
55973098
|
55973234
|
0.0002395
|
136
|
0.0002395
|
0.5007541
|
3
|
knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Pb_M/Pb_log2_QQ_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Pb_M/Pb_log2_volcano_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Pb_M/Pb_log2_manhattan_DMP_adj.png")

Se
DMP_Se = run_EWAS(DNAm = ComBat.Mvalues.Metals, pheno = pDatAge7Metal, var = 'Se_log2', covar = c('female_d', 'race_child2', 'age_yrs_7y_blood', 'age_mom_enroll_d', 'bmi_mom_prepreg_d', 'coll_grad', 'nullip', 'gt70k', 'smk_preg', 'Bcell_S_7y', 'CD4T_S_7y', 'CD8T_S_7y', 'Neu_S_7y', 'Mono_S_7y', 'NK_S_7y'), anno = anno, path = '/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Se')
# Unadjusted, N = 333
# Unadjusted, p<0.05: 17270
# Unadjusted, FDR<0.05: 1
# Unadjusted, pBonf<0.05: 1
# Adjusted, N = 333
# Adjusted, p<0.05: 20323
# Adjusted, FDR<0.05: 4
# Adjusted, pBonf<0.05: 1
# Adjusted, lambda: 0.973855
# Number of DMRs identified: 3
# rm(DMP_Se); gc()
FDR-significant DMPs
|
|
cpg
|
logFC
|
CI.L
|
CI.R
|
AveExpr
|
t
|
P.Value
|
adj.P.Val
|
B
|
adj.P.Val.bonf
|
std_err
|
chr
|
pos
|
gene
|
end
|
|
138326
|
cg08760128
|
0.2026753
|
0.1259450
|
0.2794056
|
6.725058
|
5.196935
|
4e-07
|
0.0449466
|
4.356067
|
0.1436282
|
0.0387600
|
chr16
|
4723507
|
MGRN1;MGRN1;MGRN1;MGRN1
|
4723507
|
|
157990
|
cg10145926
|
0.5456661
|
0.3464279
|
0.7449044
|
5.306680
|
5.388525
|
1e-07
|
0.0274488
|
5.040732
|
0.0548975
|
0.1015708
|
chr14
|
95875792
|
C14orf139
|
95875792
|
|
202444
|
cg13434714
|
-0.4219050
|
-0.5657148
|
-0.2780953
|
-5.770270
|
-5.772209
|
0e+00
|
0.0073738
|
6.470917
|
0.0073738
|
0.0732155
|
chr12
|
6936787
|
LEPREL2
|
6936787
|
|
381104
|
cg26708724
|
0.5887632
|
0.3639014
|
0.8136251
|
6.732563
|
5.151581
|
5e-07
|
0.0449466
|
4.196202
|
0.1797863
|
0.1146694
|
chr4
|
187509785
|
FAT1
|
187509785
|
DMRs
|
chr
|
start
|
end
|
p
|
length
|
fdr
|
sidak
|
nprobe
|
|
17
|
47091977
|
47092178
|
0
|
201
|
0
|
3.70e-06
|
4
|
|
19
|
50194119
|
50194252
|
0
|
133
|
0
|
1.48e-05
|
5
|
|
6
|
49681177
|
49681391
|
0
|
214
|
0
|
2.69e-05
|
7
|
knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Se/Se_log2_QQ_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Se/Se_log2_volcano_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Se/Se_log2_manhattan_DMP_adj.png")

Se, female
DMP_Se_F = run_EWAS(DNAm = ComBat.Mvalues.Metals, pheno = pDatAge7Metal_F, var = 'Se_log2', covar = c('race_child2', 'age_yrs_7y_blood', 'age_mom_enroll_d', 'bmi_mom_prepreg_d', 'coll_grad', 'nullip', 'gt70k', 'smk_preg', 'Bcell_S_7y', 'CD4T_S_7y', 'CD8T_S_7y', 'Neu_S_7y', 'Mono_S_7y', 'NK_S_7y'), anno = anno, path = '/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Se_F')
# Unadjusted, N = 158
# Unadjusted, p<0.05: 26254
# Unadjusted, FDR<0.05: 9
# Unadjusted, pBonf<0.05: 2
# Adjusted, N = 158
# Adjusted, p<0.05: 16021
# Adjusted, FDR<0.05: 0
# Adjusted, pBonf<0.05: 0
# Adjusted, lambda: 0.9294051
# Number of DMRs identified: 3
# rm(DMP_Se_F); gc()
DMRs
|
chr
|
start
|
end
|
p
|
length
|
fdr
|
sidak
|
nprobe
|
|
6
|
49681177
|
49681391
|
0
|
214
|
0
|
7.00e-07
|
7
|
|
10
|
38146245
|
38146671
|
0
|
426
|
0
|
5.00e-07
|
9
|
|
10
|
38299241
|
38299574
|
0
|
333
|
0
|
1.76e-05
|
9
|
knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Se_F/Se_log2_QQ_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Se_F/Se_log2_volcano_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Se_F/Se_log2_manhattan_DMP_adj.png")

Se, male
DMP_Se_M = run_EWAS(DNAm = ComBat.Mvalues.Metals, pheno = pDatAge7Metal_M, var = 'Se_log2', covar = c('race_child2', 'age_yrs_7y_blood', 'age_mom_enroll_d', 'bmi_mom_prepreg_d', 'coll_grad', 'nullip', 'gt70k', 'smk_preg', 'Bcell_S_7y', 'CD4T_S_7y', 'CD8T_S_7y', 'Neu_S_7y', 'Mono_S_7y', 'NK_S_7y'), anno = anno, path = '/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Se_M')
# Unadjusted, N = 175
# Unadjusted, p<0.05: 15593
# Unadjusted, FDR<0.05: 42
# Unadjusted, pBonf<0.05: 12
# Adjusted, N = 175
# Adjusted, p<0.05: 14283
# Adjusted, FDR<0.05: 28
# Adjusted, pBonf<0.05: 7
# Adjusted, lambda: 0.8126609
# Number of DMRs identified: 3
# rm(DMP_Se_M); gc()
FDR-significant DMPs
|
|
cpg
|
logFC
|
CI.L
|
CI.R
|
AveExpr
|
t
|
P.Value
|
adj.P.Val
|
B
|
adj.P.Val.bonf
|
std_err
|
chr
|
pos
|
gene
|
end
|
|
15593
|
cg00908120
|
0.5923048
|
0.3575326
|
0.8270770
|
6.2892750
|
4.982761
|
1.6e-06
|
0.0400205
|
1.992248
|
0.6403278
|
0.1194751
|
chr16
|
72872925
|
ZFHX3;ZFHX3
|
72872925
|
|
17338
|
cg01007589
|
0.7711724
|
0.4682737
|
1.0740712
|
4.7896683
|
5.028349
|
1.3e-06
|
0.0363003
|
2.109738
|
0.5219828
|
0.1543716
|
chr19
|
49894178
|
CCDC155
|
49894178
|
|
26849
|
cg01588060
|
-0.2710911
|
-0.3758947
|
-0.1662874
|
-5.9018630
|
-5.108606
|
9.0e-07
|
0.0301990
|
2.319787
|
0.3623878
|
0.0524668
|
chr6
|
2245749
|
GMDS;GMDS
|
2245749
|
|
76780
|
cg04692924
|
-0.5882409
|
-0.7990174
|
-0.3774643
|
-6.5844679
|
-5.511938
|
1.0e-07
|
0.0077706
|
3.394618
|
0.0555090
|
0.1071685
|
chr1
|
161720042
|
DUSP12
|
161720042
|
|
82479
|
cg05051957
|
-0.6574367
|
-0.8740830
|
-0.4407904
|
-5.6069817
|
-5.993411
|
0.0e+00
|
0.0013886
|
4.736594
|
0.0052603
|
0.1101799
|
chr8
|
141522459
|
CHRAC1;CHRAC1
|
141522459
|
|
107200
|
cg06723863
|
-0.3421497
|
-0.4652900
|
-0.2190094
|
-5.9860381
|
-5.487563
|
2.0e-07
|
0.0077706
|
3.330366
|
0.0621651
|
0.0620145
|
chr16
|
68270129
|
ESRP2;ESRP2
|
68270129
|
|
121260
|
cg07599133
|
-0.3416695
|
-0.4778828
|
-0.2054563
|
-5.9551590
|
-4.953937
|
1.8e-06
|
0.0427492
|
1.919754
|
0.7267357
|
0.0687928
|
chr19
|
35068628
|
LOC643719
|
35068628
|
|
178008
|
cg11608893
|
0.8339746
|
0.5460968
|
1.1218524
|
6.0805801
|
5.721582
|
1.0e-07
|
0.0040380
|
3.971861
|
0.0201898
|
0.1466815
|
chr6
|
32059542
|
TNXB
|
32059542
|
|
186947
|
cg12243007
|
0.4392467
|
0.2665983
|
0.6118950
|
-0.7662192
|
5.024766
|
1.3e-06
|
0.0363003
|
2.100794
|
0.5302302
|
0.0875896
|
chr17
|
184018
|
RPH3AL
|
184018
|
|
195368
|
cg12897502
|
-0.8409766
|
-1.1581637
|
-0.5237896
|
6.1025868
|
-5.236485
|
5.0e-07
|
0.0183820
|
2.654338
|
0.2022023
|
0.1616851
|
chr8
|
67425316
|
C8orf46
|
67425316
|
|
202444
|
cg13434714
|
-0.6278713
|
-0.8074616
|
-0.4482811
|
-5.7834106
|
-6.904931
|
0.0e+00
|
0.0000225
|
7.412530
|
0.0000450
|
0.0911537
|
chr12
|
6936787
|
LEPREL2
|
6936787
|
|
250632
|
cg16656826
|
0.2945037
|
0.1786042
|
0.4104032
|
0.1436170
|
5.018486
|
1.4e-06
|
0.0363003
|
2.085783
|
0.5445052
|
0.0582509
|
chr5
|
159343871
|
ADRA1B;ADRA1B
|
159343871
|
|
273355
|
cg18377660
|
0.7105200
|
0.4530993
|
0.9679406
|
5.6482645
|
5.451354
|
2.0e-07
|
0.0082254
|
3.229974
|
0.0740287
|
0.1310822
|
chr1
|
57535755
|
DAB1
|
57535755
|
|
281545
|
cg19005275
|
0.5865429
|
0.3677768
|
0.8053089
|
4.2897154
|
5.295308
|
4.0e-07
|
0.0153969
|
2.810608
|
0.1539686
|
0.1112673
|
chr12
|
113588263
|
CCDC42B
|
113588263
|
|
311691
|
cg21373263
|
0.8225623
|
0.5510102
|
1.0941144
|
3.2926911
|
5.982561
|
0.0e+00
|
0.0013886
|
4.705737
|
0.0055543
|
0.1383211
|
chr10
|
126751982
|
CTBP2;CTBP2
|
126751982
|
|
359398
|
cg25067702
|
-0.6449717
|
-0.8730675
|
-0.4168760
|
-6.4012877
|
-5.584637
|
1.0e-07
|
0.0065319
|
3.593491
|
0.0391915
|
0.1160520
|
chr17
|
70723227
|
SLC39A11;SLC39A11
|
70723227
|
|
381104
|
cg26708724
|
1.0174549
|
0.7331142
|
1.3017956
|
6.7173655
|
7.067202
|
0.0e+00
|
0.0000186
|
7.903550
|
0.0000186
|
0.1448704
|
chr4
|
187509785
|
FAT1
|
187509785
|
DMRs
|
chr
|
start
|
end
|
p
|
length
|
fdr
|
sidak
|
nprobe
|
|
17
|
70723226
|
70723386
|
0.0000000
|
160
|
0.0000000
|
0.0000001
|
2
|
|
4
|
24796918
|
24797176
|
0.0000000
|
258
|
0.0000000
|
0.0000212
|
6
|
|
10
|
121578383
|
121578639
|
0.0000001
|
256
|
0.0000001
|
0.0001182
|
3
|
|
6
|
30039141
|
30039175
|
0.0047996
|
34
|
0.0047996
|
1.0000000
|
3
|
knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Se_M/Se_log2_QQ_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Se_M/Se_log2_volcano_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Se_M/Se_log2_manhattan_DMP_adj.png")

Zn
DMP_Zn = run_EWAS(DNAm = ComBat.Mvalues.Metals, pheno = pDatAge7Metal, var = 'Zn_log2', covar = c('female_d', 'race_child2', 'age_yrs_7y_blood', 'age_mom_enroll_d', 'bmi_mom_prepreg_d', 'coll_grad', 'nullip', 'gt70k', 'smk_preg', 'Bcell_S_7y', 'CD4T_S_7y', 'CD8T_S_7y', 'Neu_S_7y', 'Mono_S_7y', 'NK_S_7y'), anno = anno, path = '/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Zn')
# Unadjusted, N = 333
# Unadjusted, p<0.05: 12854
# Unadjusted, FDR<0.05: 1
# Unadjusted, pBonf<0.05: 1
# Adjusted, N = 333
# Adjusted, p<0.05: 23377
# Adjusted, FDR<0.05: 13
# Adjusted, pBonf<0.05: 3
# Adjusted, lambda: 1.10425
# Number of DMRs identified: 13
# rm(DMP_Zn); gc()
FDR-significant DMPs
|
|
cpg
|
logFC
|
CI.L
|
CI.R
|
AveExpr
|
t
|
P.Value
|
adj.P.Val
|
B
|
adj.P.Val.bonf
|
std_err
|
chr
|
pos
|
gene
|
end
|
|
1551
|
cg00082497
|
-0.2789683
|
-0.3788872
|
-0.1790494
|
-5.316840
|
-5.493142
|
1.0e-07
|
0.0116179
|
5.179846
|
0.0320645
|
0.0506389
|
chr1
|
32802133
|
MARCKSL1
|
32802133
|
|
15593
|
cg00908120
|
0.4887949
|
0.3055657
|
0.6720241
|
6.259296
|
5.248649
|
3.0e-07
|
0.0171923
|
4.318434
|
0.1111402
|
0.0933516
|
chr16
|
72872925
|
ZFHX3;ZFHX3
|
72872925
|
|
66105
|
cg04015129
|
0.6544048
|
0.3991261
|
0.9096834
|
4.283036
|
5.043681
|
8.0e-07
|
0.0293642
|
3.620884
|
0.3043451
|
0.1301901
|
chr10
|
1058036
|
GTPBP4
|
1058036
|
|
90290
|
cg05573434
|
0.4125276
|
0.2574161
|
0.5676391
|
-3.154237
|
5.232686
|
3.0e-07
|
0.0171923
|
4.263312
|
0.1203459
|
0.0789613
|
chr4
|
7648540
|
SORCS2
|
7648540
|
|
107200
|
cg06723863
|
-0.2528131
|
-0.3544065
|
-0.1512197
|
-5.982133
|
-4.896069
|
1.6e-06
|
0.0473985
|
3.132897
|
0.6161801
|
0.0515011
|
chr16
|
68270129
|
ESRP2;ESRP2
|
68270129
|
|
133940
|
cg08459368
|
0.5943151
|
0.3801796
|
0.8084505
|
2.645733
|
5.460643
|
1.0e-07
|
0.0116179
|
5.062990
|
0.0379479
|
0.1091583
|
chr11
|
61974948
|
SCGB2A1
|
61974948
|
|
165306
|
cg10653573
|
0.8207249
|
0.5017201
|
1.1397297
|
5.432304
|
5.061929
|
7.0e-07
|
0.0293642
|
3.682080
|
0.2785931
|
0.1627524
|
chr8
|
141347297
|
TRAPPC9;TRAPPC9
|
141347297
|
|
202444
|
cg13434714
|
-0.4872777
|
-0.6443364
|
-0.3302191
|
-5.770270
|
-6.104221
|
0.0e+00
|
0.0011936
|
7.460402
|
0.0011936
|
0.0799582
|
chr12
|
6936787
|
LEPREL2
|
6936787
|
|
234745
|
cg15528091
|
-0.3070787
|
-0.4271830
|
-0.1869744
|
-6.355947
|
-5.030429
|
8.0e-07
|
0.0293642
|
3.577005
|
0.3242929
|
0.0610193
|
chr19
|
18119069
|
ARRDC2;ARRDC2;ARRDC2
|
18119069
|
|
248112
|
cg16496814
|
0.2140204
|
0.1314881
|
0.2965527
|
5.206564
|
5.102050
|
6.0e-07
|
0.0286288
|
3.817765
|
0.2290303
|
0.0416708
|
chr11
|
9778721
|
|
9778721
|
|
281636
|
cg19011752
|
0.2463497
|
0.1496666
|
0.3430328
|
-2.537801
|
5.013200
|
9.0e-07
|
0.0293642
|
3.519541
|
0.3523705
|
0.0489723
|
chr21
|
45772638
|
TRPM2
|
45772638
|
|
338217
|
cg23477849
|
0.2605321
|
0.1652481
|
0.3558161
|
4.877957
|
5.379658
|
1.0e-07
|
0.0116179
|
4.776453
|
0.0573879
|
0.0482514
|
chr19
|
5698492
|
LONP1
|
5698492
|
|
370410
|
cg25954729
|
-0.2155491
|
-0.2944166
|
-0.1366816
|
-6.344974
|
-5.377269
|
1.0e-07
|
0.0116179
|
4.768033
|
0.0580895
|
0.0397755
|
chr11
|
66610784
|
RCE1;C11orf80;RCE1
|
66610784
|
DMRs
|
chr
|
start
|
end
|
p
|
length
|
fdr
|
sidak
|
nprobe
|
|
12
|
54070516
|
54070610
|
0.0000000
|
94
|
0.0000000
|
0.0000052
|
5
|
|
19
|
18118799
|
18119069
|
0.0000000
|
270
|
0.0000000
|
0.0000098
|
3
|
|
10
|
124638975
|
124639260
|
0.0000000
|
285
|
0.0000001
|
0.0000233
|
12
|
|
20
|
25129295
|
25129562
|
0.0000001
|
267
|
0.0000002
|
0.0001003
|
8
|
|
6
|
32063990
|
32064258
|
0.0000001
|
268
|
0.0000002
|
0.0001031
|
12
|
|
4
|
7648539
|
7648627
|
0.0000001
|
88
|
0.0000002
|
0.0003372
|
2
|
|
8
|
41655672
|
41655894
|
0.0000001
|
222
|
0.0000002
|
0.0002389
|
4
|
|
6
|
41168800
|
41169049
|
0.0000001
|
249
|
0.0000002
|
0.0002207
|
6
|
|
17
|
1395863
|
1396123
|
0.0000002
|
260
|
0.0000002
|
0.0002547
|
5
|
|
17
|
79503641
|
79503877
|
0.0000002
|
236
|
0.0000002
|
0.0002943
|
4
|
|
12
|
54385274
|
54385526
|
0.0000002
|
252
|
0.0000002
|
0.0002909
|
4
|
|
22
|
45704987
|
45705042
|
0.0000002
|
55
|
0.0000002
|
0.0014895
|
4
|
|
20
|
35169593
|
35169846
|
0.0004351
|
253
|
0.0004351
|
0.4926596
|
3
|
knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Zn/Zn_log2_QQ_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Zn/Zn_log2_volcano_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Zn/Zn_log2_manhattan_DMP_adj.png")

Zn, female
DMP_Zn_F = run_EWAS(DNAm = ComBat.Mvalues.Metals, pheno = pDatAge7Metal_F, var = 'Zn_log2', covar = c('race_child2', 'age_yrs_7y_blood', 'age_mom_enroll_d', 'bmi_mom_prepreg_d', 'coll_grad', 'nullip', 'gt70k', 'smk_preg', 'Bcell_S_7y', 'CD4T_S_7y', 'CD8T_S_7y', 'Neu_S_7y', 'Mono_S_7y', 'NK_S_7y'), anno = anno, path = '/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Zn_F')
# # Unadjusted, N = 158
# Unadjusted, p<0.05: 12830
# Unadjusted, FDR<0.05: 0
# Unadjusted, pBonf<0.05: 0
# Adjusted, N = 158
# Adjusted, p<0.05: 17143
# Adjusted, FDR<0.05: 0
# Adjusted, pBonf<0.05: 0
# Adjusted, lambda: 0.9412223
# Number of DMRs identified: 3
# rm(DMP_Zn_F); gc()
DMRs
|
chr
|
start
|
end
|
p
|
length
|
fdr
|
sidak
|
nprobe
|
|
11
|
73357018
|
73357396
|
0.0e+00
|
378
|
0.0e+00
|
0.0000000
|
8
|
|
1
|
120174148
|
120174361
|
7.0e-07
|
213
|
1.1e-06
|
0.0013294
|
2
|
|
10
|
124638975
|
124639012
|
1.1e-05
|
37
|
1.1e-05
|
0.1109657
|
4
|
knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Zn_F/Zn_log2_QQ_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Zn_F/Zn_log2_volcano_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Zn_F/Zn_log2_manhattan_DMP_adj.png")

Zn, male
DMP_Zn_M = run_EWAS(DNAm = ComBat.Mvalues.Metals, pheno = pDatAge7Metal_M, var = 'Zn_log2', covar = c('race_child2', 'age_yrs_7y_blood', 'age_mom_enroll_d', 'bmi_mom_prepreg_d', 'coll_grad', 'nullip', 'gt70k', 'smk_preg', 'Bcell_S_7y', 'CD4T_S_7y', 'CD8T_S_7y', 'Neu_S_7y', 'Mono_S_7y', 'NK_S_7y'), anno = anno, path = '/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Zn_M')
# Unadjusted, N = 175
# Unadjusted, p<0.05: 16787
# Unadjusted, FDR<0.05: 36
# Unadjusted, pBonf<0.05: 8
# Adjusted, N = 175
# Adjusted, p<0.05: 14737
# Adjusted, FDR<0.05: 36
# Adjusted, pBonf<0.05: 3
# Adjusted, lambda: 0.8766913
# Number of DMRs identified: 16
# rm(DMP_Zn_M); gc()
FDR-significant DMPs
|
|
cpg
|
logFC
|
CI.L
|
CI.R
|
AveExpr
|
t
|
P.Value
|
adj.P.Val
|
B
|
adj.P.Val.bonf
|
std_err
|
chr
|
pos
|
gene
|
end
|
|
15593
|
cg00908120
|
0.7986746
|
0.5264258
|
1.0709234
|
6.2892750
|
5.793958
|
0.0e+00
|
0.0052948
|
3.3135597
|
0.0141641
|
0.1385227
|
chr16
|
72872925
|
ZFHX3;ZFHX3
|
72872925
|
|
17338
|
cg01007589
|
0.9065622
|
0.5465007
|
1.2666237
|
4.7896683
|
4.972701
|
1.7e-06
|
0.0267901
|
1.3379386
|
0.6697528
|
0.1835056
|
chr19
|
49894178
|
CCDC155
|
49894178
|
|
18335
|
cg01063965
|
-0.2692683
|
-0.3808800
|
-0.1576566
|
-6.4353826
|
-4.764741
|
4.2e-06
|
0.0451214
|
0.8668535
|
1.0000000
|
0.0555811
|
chr11
|
695461
|
TMEM80;TMEM80;DEAF1;DEAF1
|
695461
|
|
24635
|
cg01447660
|
0.4161258
|
0.2471860
|
0.5850656
|
-0.9207246
|
4.864703
|
2.7e-06
|
0.0334209
|
1.0923878
|
1.0000000
|
0.0854122
|
chr2
|
69152678
|
|
69152678
|
|
25935
|
cg01533258
|
-0.3013596
|
-0.4269158
|
-0.1758034
|
-6.4562972
|
-4.740350
|
4.7e-06
|
0.0463873
|
0.8122693
|
1.0000000
|
0.0628818
|
chr14
|
95235489
|
GSC
|
95235489
|
|
36678
|
cg02196294
|
-0.2906897
|
-0.4099158
|
-0.1714636
|
-5.4126781
|
-4.815283
|
3.4e-06
|
0.0372147
|
0.9805256
|
1.0000000
|
0.0595727
|
chr6
|
39197260
|
KCNK5
|
39197260
|
|
41497
|
cg02490920
|
0.3948042
|
0.2423949
|
0.5472136
|
1.3358885
|
5.116039
|
9.0e-07
|
0.0166832
|
1.6720694
|
0.3503468
|
0.0768511
|
chr3
|
50304406
|
SEMA3B;SEMA3B
|
50304406
|
|
45187
|
cg02711608
|
0.5447487
|
0.3462840
|
0.7432134
|
-2.0855657
|
5.421025
|
2.0e-07
|
0.0122834
|
2.3968616
|
0.0853542
|
0.1006441
|
chr19
|
47287964
|
SLC1A5;SLC1A5;SLC1A5;SLC1A5
|
47287964
|
|
49479
|
cg02968175
|
0.3308394
|
0.2054185
|
0.4562602
|
5.7555141
|
5.209681
|
6.0e-07
|
0.0127085
|
1.8924369
|
0.2282507
|
0.0628111
|
chr16
|
4690020
|
MGRN1;MGRN1;MGRN1;MGRN1
|
4690020
|
|
55565
|
cg03352332
|
0.8979978
|
0.5628181
|
1.2331775
|
5.5379777
|
5.291381
|
4.0e-07
|
0.0123746
|
2.0848241
|
0.1568056
|
0.1707666
|
chr3
|
186360953
|
FETUB
|
186360953
|
|
66105
|
cg04015129
|
0.8663699
|
0.5510958
|
1.1816440
|
4.2710633
|
5.427334
|
2.0e-07
|
0.0122834
|
2.4113963
|
0.0829347
|
0.1605719
|
chr10
|
1058036
|
GTPBP4
|
1058036
|
|
71895
|
cg04374006
|
0.2627697
|
0.1559793
|
0.3695602
|
-0.2704598
|
4.859668
|
2.8e-06
|
0.0334209
|
1.0809686
|
1.0000000
|
0.0530461
|
chr19
|
33556395
|
RHPN2
|
33556395
|
|
72385
|
cg04406071
|
-0.3235390
|
-0.4464810
|
-0.2005970
|
-6.0707229
|
-5.197446
|
6.0e-07
|
0.0127085
|
1.8635148
|
0.2414621
|
0.0615161
|
chr17
|
59489784
|
C17orf82
|
59489784
|
|
76780
|
cg04692924
|
-0.6620566
|
-0.9146336
|
-0.4094796
|
-6.5844679
|
-5.176935
|
7.0e-07
|
0.0132956
|
1.8135106
|
0.2659111
|
0.1284330
|
chr1
|
161720042
|
DUSP12
|
161720042
|
|
82479
|
cg05051957
|
-0.6556186
|
-0.9211778
|
-0.3900594
|
-5.6069817
|
-4.875974
|
2.6e-06
|
0.0334209
|
1.1167256
|
1.0000000
|
0.1350923
|
chr8
|
141522459
|
CHRAC1;CHRAC1
|
141522459
|
|
107200
|
cg06723863
|
-0.3660155
|
-0.5147452
|
-0.2172859
|
-5.9860381
|
-4.860330
|
2.8e-06
|
0.0334209
|
1.0824690
|
1.0000000
|
0.0749420
|
chr16
|
68270129
|
ESRP2;ESRP2
|
68270129
|
|
117957
|
cg07380021
|
-0.6557600
|
-0.9015723
|
-0.4099477
|
-5.4253082
|
-5.268813
|
4.0e-07
|
0.0124371
|
2.0310571
|
0.1741199
|
0.1249619
|
chr1
|
206755252
|
RASSF5;RASSF5;RASSF5
|
206755252
|
|
138326
|
cg08760128
|
0.3591892
|
0.2311150
|
0.4872635
|
6.7313293
|
5.538922
|
1.0e-07
|
0.0121638
|
2.6848170
|
0.0486553
|
0.0641960
|
chr16
|
4723507
|
MGRN1;MGRN1;MGRN1;MGRN1
|
4723507
|
|
143452
|
cg09127400
|
-0.3253080
|
-0.4612252
|
-0.1893909
|
-5.8091855
|
-4.726984
|
5.0e-06
|
0.0479454
|
0.7824329
|
1.0000000
|
0.0682830
|
chr6
|
30712331
|
IER3
|
30712331
|
|
159790
|
cg10266648
|
1.0393561
|
0.6292003
|
1.4495119
|
5.9758418
|
5.004802
|
1.5e-06
|
0.0241741
|
1.4119349
|
0.5801792
|
0.2091418
|
chr2
|
106560529
|
|
106560529
|
|
165306
|
cg10653573
|
1.4145550
|
0.8990686
|
1.9300414
|
5.3698793
|
5.419686
|
2.0e-07
|
0.0122834
|
2.3929054
|
0.0859836
|
0.2630143
|
chr8
|
141347297
|
TRAPPC9;TRAPPC9
|
141347297
|
|
168880
|
cg10923018
|
0.3112659
|
0.1850396
|
0.4374922
|
2.7253233
|
4.870183
|
2.7e-06
|
0.0334209
|
1.1048470
|
1.0000000
|
0.0632316
|
chr6
|
31743769
|
C6orf27
|
31743769
|
|
180170
|
cg11761483
|
-0.7173589
|
-0.9874920
|
-0.4472257
|
-5.5960630
|
-5.244814
|
5.0e-07
|
0.0127085
|
1.9740228
|
0.1945730
|
0.1374378
|
chr17
|
70723386
|
SLC39A11;SLC39A11
|
70723386
|
|
202444
|
cg13434714
|
-0.8386175
|
-1.0430621
|
-0.6341729
|
-5.7834106
|
-8.101361
|
0.0e+00
|
0.0000001
|
9.4776845
|
0.0000001
|
0.1037179
|
chr12
|
6936787
|
LEPREL2
|
6936787
|
|
216196
|
cg14230280
|
1.2229340
|
0.7320030
|
1.7138651
|
4.2784975
|
4.919874
|
2.1e-06
|
0.0313748
|
1.2167946
|
0.8471192
|
0.2504580
|
chr9
|
132502800
|
PTGES
|
132502800
|
|
248112
|
cg16496814
|
0.3215835
|
0.2022500
|
0.4409170
|
5.2206210
|
5.322247
|
3.0e-07
|
0.0123746
|
2.1603427
|
0.1354705
|
0.0596289
|
chr11
|
9778721
|
|
9778721
|
|
250632
|
cg16656826
|
0.3445219
|
0.2066488
|
0.4823949
|
0.1436170
|
4.935159
|
2.0e-06
|
0.0303861
|
1.2531114
|
0.7900373
|
0.0693009
|
chr5
|
159343871
|
ADRA1B;ADRA1B
|
159343871
|
|
257216
|
cg17155018
|
-1.0196926
|
-1.4432541
|
-0.5961312
|
1.3941337
|
-4.754713
|
4.4e-06
|
0.0455985
|
0.8432207
|
1.0000000
|
0.2160003
|
chr6
|
111953066
|
|
111953066
|
|
268589
|
cg18037826
|
0.4119927
|
0.2555297
|
0.5684556
|
4.2937576
|
5.200460
|
6.0e-07
|
0.0127085
|
1.8706351
|
0.2381405
|
0.0789525
|
chr12
|
109273835
|
DAO
|
109273835
|
|
281545
|
cg19005275
|
0.7482069
|
0.4921296
|
1.0042842
|
4.2897154
|
5.770615
|
0.0e+00
|
0.0052948
|
3.2552389
|
0.0158843
|
0.1302288
|
chr12
|
113588263
|
CCDC42B
|
113588263
|
|
286872
|
cg19439837
|
0.9459971
|
0.5527040
|
1.3392901
|
6.9655374
|
4.750562
|
4.5e-06
|
0.0455985
|
0.8339344
|
1.0000000
|
0.2005136
|
chr12
|
4923529
|
KCNA6;KCNA6
|
4923529
|
|
288096
|
cg19532212
|
0.7606680
|
0.4803455
|
1.0409904
|
4.4209486
|
5.359308
|
3.0e-07
|
0.0123746
|
2.2474246
|
0.1142103
|
0.1426619
|
chr17
|
56769430
|
TEX14;RAD51C;TEX14;RAD51C
|
56769430
|
|
311691
|
cg21373263
|
0.8805707
|
0.5515533
|
1.2095881
|
3.2926911
|
5.285874
|
4.0e-07
|
0.0123746
|
2.0716919
|
0.1608692
|
0.1676110
|
chr10
|
126751982
|
CTBP2;CTBP2
|
126751982
|
|
322216
|
cg22240394
|
1.2229725
|
0.7670216
|
1.6789234
|
6.8239404
|
5.297489
|
4.0e-07
|
0.0123746
|
2.0993979
|
0.1524156
|
0.2325683
|
chr3
|
186211630
|
|
186211630
|
|
324251
|
cg22413938
|
-0.3880547
|
-0.5460152
|
-0.2300942
|
-4.5630336
|
-4.851858
|
2.9e-06
|
0.0335705
|
1.0632521
|
1.0000000
|
0.0797285
|
chr14
|
78447481
|
|
78447481
|
|
338217
|
cg23477849
|
0.3810081
|
0.2311925
|
0.5308237
|
4.8962493
|
5.022741
|
1.4e-06
|
0.0232259
|
1.4548453
|
0.5341954
|
0.0755056
|
chr19
|
5698492
|
LONP1
|
5698492
|
|
339781
|
cg23601521
|
0.7996758
|
0.4972086
|
1.1021431
|
4.8708259
|
5.221641
|
5.0e-07
|
0.0127085
|
1.9190935
|
0.2165310
|
0.1540110
|
chr2
|
50275179
|
NRXN1;NRXN1;NRXN1
|
50275179
|
|
370410
|
cg25954729
|
-0.3034838
|
-0.4163024
|
-0.1906653
|
-6.3724574
|
-5.312742
|
4.0e-07
|
0.0123746
|
2.1375974
|
0.1416105
|
0.0562146
|
chr11
|
66610784
|
RCE1;C11orf80;RCE1
|
66610784
|
|
379632
|
cg26608798
|
0.3969674
|
0.2358372
|
0.5580975
|
0.5750420
|
4.865660
|
2.7e-06
|
0.0334209
|
1.0945703
|
1.0000000
|
0.0813703
|
chr16
|
33853544
|
|
33853544
|
|
381104
|
cg26708724
|
0.9252394
|
0.5664932
|
1.2839856
|
6.7173655
|
5.093758
|
1.0e-06
|
0.0176594
|
1.6184667
|
0.3885072
|
0.1828323
|
chr4
|
187509785
|
FAT1
|
187509785
|
|
392164
|
cg27503275
|
0.4776627
|
0.2828083
|
0.6725171
|
4.1214740
|
4.841489
|
3.0e-06
|
0.0341627
|
1.0390945
|
1.0000000
|
0.0987864
|
chr6
|
3880016
|
|
3880016
|
DMRs
|
chr
|
start
|
end
|
p
|
length
|
fdr
|
sidak
|
nprobe
|
|
17
|
70723226
|
70723386
|
0.0000000
|
160
|
0.0000000
|
0.0000026
|
2
|
|
10
|
121578136
|
121578639
|
0.0000000
|
503
|
0.0000000
|
0.0000012
|
4
|
|
14
|
78447480
|
78447640
|
0.0000000
|
160
|
0.0000000
|
0.0000126
|
3
|
|
19
|
50194119
|
50194252
|
0.0000000
|
133
|
0.0000000
|
0.0000160
|
5
|
|
4
|
186732836
|
186733060
|
0.0000000
|
224
|
0.0000000
|
0.0000130
|
7
|
|
4
|
24796918
|
24797176
|
0.0000000
|
258
|
0.0000000
|
0.0000182
|
6
|
|
14
|
76734326
|
76734605
|
0.0000000
|
279
|
0.0000000
|
0.0000220
|
5
|
|
21
|
45773781
|
45773997
|
0.0000000
|
216
|
0.0000000
|
0.0000374
|
2
|
|
5
|
135416204
|
135416613
|
0.0000000
|
409
|
0.0000000
|
0.0000256
|
9
|
|
11
|
63679431
|
63679637
|
0.0000001
|
206
|
0.0000001
|
0.0001231
|
2
|
|
20
|
62716331
|
62716606
|
0.0000001
|
275
|
0.0000001
|
0.0001330
|
4
|
|
17
|
78549323
|
78549371
|
0.0000001
|
48
|
0.0000002
|
0.0011147
|
3
|
|
5
|
1868136
|
1868357
|
0.0000004
|
221
|
0.0000005
|
0.0007368
|
4
|
|
22
|
45704987
|
45705042
|
0.0000015
|
55
|
0.0000017
|
0.0104801
|
4
|
|
5
|
176755392
|
176755449
|
0.0000127
|
57
|
0.0000135
|
0.0839213
|
2
|
|
2
|
88583556
|
88583805
|
0.0001042
|
249
|
0.0001042
|
0.1522101
|
3
|
knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Zn_M/Zn_log2_QQ_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Zn_M/Zn_log2_volcano_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Zn_M/Zn_log2_manhattan_DMP_adj.png")
